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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs7316

Current Build 154

Released April 21, 2020

Organism
Homo sapiens
Position
chr2:85658890 (GRCh38.p12) Help

The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.

Alleles
T>A / T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.149130 (18726/125568, TOPMED)
C=0.098414 (10945/111214, ALFA Project)
C=0.13677 (4288/31352, GnomAD) (+ 15 more)
C=0.1769 (886/5008, 1000G)
C=0.0846 (379/4480, Estonian)
C=0.0719 (277/3854, ALSPAC)
C=0.0796 (295/3708, TWINSUK)
C=0.2329 (682/2928, KOREAN)
C=0.2069 (391/1890, HapMap)
C=0.2418 (443/1832, Korea1K)
C=0.081 (81/998, GoNL)
C=0.152 (95/626, Chileans)
C=0.062 (37/600, NorthernSweden)
C=0.116 (25/216, Qatari)
C=0.192 (41/214, Vietnamese)
T=0.367 (72/196, SGDP_PRJ)
C=0.15 (6/40, GENOME_DK)
T=0.45 (10/22, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SFTPB : Intron Variant
Publications
4 citations
Genomic View
See rs on genome
Help

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements
Sequence name Change
GRCh38.p12 chr 2 NC_000002.12:g.85658890T>A
GRCh38.p12 chr 2 NC_000002.12:g.85658890T>C
GRCh37.p13 chr 2 NC_000002.11:g.85886013T>A
GRCh37.p13 chr 2 NC_000002.11:g.85886013T>C
SFTPB RefSeqGene NG_016967.1:g.14852A>T
SFTPB RefSeqGene NG_016967.1:g.14852A>G
Gene: SFTPB, surfactant protein B (minus strand)
Molecule type Change Amino acid[Codon] SO Term
SFTPB transcript variant 3 NM_001367281.1:c.1003-35A…

NM_001367281.1:c.1003-35A>T

N/A Intron Variant
SFTPB transcript variant 2 NM_198843.3:c.*20-35A>T N/A Intron Variant
SFTPB transcript variant 1 NM_000542.5:c.*812= N/A 3 Prime UTR Variant
SFTPB transcript variant X1 XM_005264487.2:c.*856= N/A 3 Prime UTR Variant
SFTPB transcript variant X2 XM_005264488.4:c.*812= N/A 3 Prime UTR Variant
SFTPB transcript variant X3 XM_005264490.4:c. N/A Genic Downstream Transcript Variant
Help

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Not Reported in ClinVar

ALFA Allele Frequency (New)
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 257574 T=0.905429 C=0.094571
European Sub 223058 T=0.921021 C=0.078979
African Sub 11236 T=0.75400 C=0.24600
African Others Sub 388 T=0.768 C=0.232
African American Sub 10848 T=0.75350 C=0.24650
Asian Sub 3854 T=0.7514 C=0.2486
East Asian Sub 3092 T=0.7701 C=0.2299
Other Asian Sub 762 T=0.676 C=0.324
Latin American 1 Sub 1174 T=0.8586 C=0.1414
Latin American 2 Sub 8750 T=0.8173 C=0.1827
South Asian Sub 378 T=0.926 C=0.074
Other Sub 9124 T=0.8655 C=0.1345


Help

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 125568 T=0.850870 C=0.149130
ALFA Total Global 111214 T=0.901586 C=0.098414
ALFA European Sub 93262 T=0.92114 C=0.07886
ALFA Latin American 2 Sub 7526 T=0.8152 C=0.1848
ALFA African Sub 6354 T=0.7520 C=0.2480
ALFA Other Sub 3028 T=0.8501 C=0.1499
ALFA Latin American 1 Sub 690 T=0.861 C=0.139
ALFA Asian Sub 278 T=0.759 C=0.241
ALFA South Asian Sub 76 T=0.92 C=0.08
gnomAD - Genomes Global Study-wide 31352 T=0.86323 C=0.13677
gnomAD - Genomes European Sub 18894 T=0.92230 C=0.07770
gnomAD - Genomes African Sub 8684 T=0.7576 C=0.2424
gnomAD - Genomes East Asian Sub 1552 T=0.7513 C=0.2487
gnomAD - Genomes Other Sub 1088 T=0.8906 C=0.1094
gnomAD - Genomes American Sub 844 T=0.773 C=0.227
gnomAD - Genomes Ashkenazi Jewish Sub 290 T=0.938 C=0.062
1000Genomes Global Study-wide 5008 T=0.8231 C=0.1769
1000Genomes African Sub 1322 T=0.7368 C=0.2632
1000Genomes East Asian Sub 1008 T=0.7778 C=0.2222
1000Genomes Europe Sub 1006 T=0.8956 C=0.1044
1000Genomes South Asian Sub 978 T=0.935 C=0.065
1000Genomes American Sub 694 T=0.791 C=0.209
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.9154 C=0.0846
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.9281 C=0.0719
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.9204 C=0.0796
KOREAN population from KRGDB KOREAN Study-wide 2928 T=0.7671 A=0.0000, C=0.2329
HapMap Global Study-wide 1890 T=0.7931 C=0.2069
HapMap American Sub 768 T=0.840 C=0.160
HapMap African Sub 692 T=0.731 C=0.269
HapMap Asian Sub 254 T=0.768 C=0.232
HapMap Europe Sub 176 T=0.869 C=0.131
Korean Genome Project KOREAN Study-wide 1832 T=0.7582 C=0.2418
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.919 C=0.081
Chileans Chilean Study-wide 626 T=0.848 C=0.152
Northern Sweden ACPOP Study-wide 600 T=0.938 C=0.062
Qatari Global Study-wide 216 T=0.884 C=0.116
A Vietnamese Genetic Variation Database Global Study-wide 214 T=0.808 C=0.192
SGDP_PRJ Global Study-wide 196 T=0.367 C=0.633
The Danish reference pan genome Danish Study-wide 40 T=0.85 C=0.15
Siberian Global Study-wide 22 T=0.45 C=0.55
Help

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement T= A C
GRCh38.p12 chr 2 NC_000002.12:g.85658890= NC_000002.12:g.85658890T>A NC_000002.12:g.85658890T>C
GRCh37.p13 chr 2 NC_000002.11:g.85886013= NC_000002.11:g.85886013T>A NC_000002.11:g.85886013T>C
SFTPB RefSeqGene NG_016967.1:g.14852= NG_016967.1:g.14852A>T NG_016967.1:g.14852A>G
SFTPB transcript variant 1 NM_000542.5:c.*812= NM_000542.5:c.*812A>T NM_000542.5:c.*812A>G
SFTPB transcript variant 1 NM_000542.4:c.*812= NM_000542.4:c.*812A>T NM_000542.4:c.*812A>G
SFTPB transcript variant 1 NM_000542.3:c.*812= NM_000542.3:c.*812A>T NM_000542.3:c.*812A>G
SFTPB transcript variant X2 XM_005264488.4:c.*812= XM_005264488.4:c.*812A>T XM_005264488.4:c.*812A>G
SFTPB transcript variant X2 XM_005264488.1:c.*812= XM_005264488.1:c.*812A>T XM_005264488.1:c.*812A>G
SFTPB transcript variant X1 XM_005264487.2:c.*856= XM_005264487.2:c.*856A>T XM_005264487.2:c.*856A>G
SFTPB transcript variant X1 XM_005264487.1:c.*856= XM_005264487.1:c.*856A>T XM_005264487.1:c.*856A>G
SFTPB transcript variant 3 NM_001367281.1:c.1003-35= NM_001367281.1:c.1003-35A>T NM_001367281.1:c.1003-35A>G
SFTPB transcript variant 2 NM_198843.2:c.*20-35= NM_198843.2:c.*20-35A>T NM_198843.2:c.*20-35A>G
SFTPB transcript variant 2 NM_198843.3:c.*20-35= NM_198843.3:c.*20-35A>T NM_198843.3:c.*20-35A>G
SFTPB transcript variant X3 XM_005264489.1:c.*20-35= XM_005264489.1:c.*20-35A>T XM_005264489.1:c.*20-35A>G
Help

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

88 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 CGAP-GAI ss9144 Sep 19, 2000 (52)
2 SC_JCM ss4116385 Nov 05, 2001 (101)
3 PGA-UW-FHCRC ss4250774 Jan 04, 2002 (102)
4 SEQUENOM ss24789670 Sep 20, 2004 (123)
5 PGA-UW-FHCRC ss52088713 Oct 16, 2006 (127)
6 AFFY ss76754306 Dec 07, 2007 (129)
7 HGSV ss77328827 Dec 07, 2007 (129)
8 KRIBB_YJKIM ss104807870 Feb 05, 2009 (130)
9 1000GENOMES ss109698942 Jan 24, 2009 (130)
10 1000GENOMES ss110594549 Jan 25, 2009 (130)
11 ILLUMINA-UK ss117791423 Feb 14, 2009 (130)
12 ILLUMINA ss160872063 Dec 01, 2009 (131)
13 COMPLETE_GENOMICS ss163719021 Jul 04, 2010 (132)
14 ILLUMINA ss174337284 Jul 04, 2010 (132)
15 BUSHMAN ss200735809 Jul 04, 2010 (132)
16 1000GENOMES ss219376195 Jul 14, 2010 (132)
17 1000GENOMES ss231262491 Jul 14, 2010 (132)
18 1000GENOMES ss238795451 Jul 15, 2010 (132)
19 GMI ss276557565 May 04, 2012 (137)
20 ILLUMINA ss481543069 May 04, 2012 (137)
21 ILLUMINA ss481572117 May 04, 2012 (137)
22 ILLUMINA ss482545341 Sep 08, 2015 (146)
23 ILLUMINA ss485566537 May 04, 2012 (137)
24 ILLUMINA ss537463265 Sep 08, 2015 (146)
25 TISHKOFF ss555718091 Apr 25, 2013 (138)
26 SSMP ss649311285 Apr 25, 2013 (138)
27 ILLUMINA ss778972170 Sep 08, 2015 (146)
28 ILLUMINA ss783228815 Sep 08, 2015 (146)
29 ILLUMINA ss784183026 Sep 08, 2015 (146)
30 ILLUMINA ss832489194 Sep 08, 2015 (146)
31 ILLUMINA ss834434233 Sep 08, 2015 (146)
32 EVA-GONL ss977083339 Aug 21, 2014 (142)
33 JMKIDD_LAB ss1069307062 Aug 21, 2014 (142)
34 1000GENOMES ss1298205381 Aug 21, 2014 (142)
35 DDI ss1428649411 Apr 01, 2015 (144)
36 EVA_GENOME_DK ss1578978158 Apr 01, 2015 (144)
37 EVA_DECODE ss1586506190 Apr 01, 2015 (144)
38 EVA_UK10K_ALSPAC ss1604028660 Apr 01, 2015 (144)
39 EVA_UK10K_TWINSUK ss1647022693 Apr 01, 2015 (144)
40 EVA_SVP ss1712473139 Apr 01, 2015 (144)
41 ILLUMINA ss1752372905 Sep 08, 2015 (146)
42 HAMMER_LAB ss1797089066 Sep 08, 2015 (146)
43 WEILL_CORNELL_DGM ss1920317203 Feb 12, 2016 (147)
44 ILLUMINA ss1946046031 Feb 12, 2016 (147)
45 ILLUMINA ss1958436749 Feb 12, 2016 (147)
46 GENOMED ss1968827053 Jul 19, 2016 (147)
47 JJLAB ss2020693313 Sep 14, 2016 (149)
48 USC_VALOUEV ss2148738217 Dec 20, 2016 (150)
49 HUMAN_LONGEVITY ss2232308925 Dec 20, 2016 (150)
50 TOPMED ss2398291606 Dec 20, 2016 (150)
51 SYSTEMSBIOZJU ss2624854235 Nov 08, 2017 (151)
52 ILLUMINA ss2633644191 Nov 08, 2017 (151)
53 GRF ss2703317873 Nov 08, 2017 (151)
54 ILLUMINA ss2710906460 Nov 08, 2017 (151)
55 GNOMAD ss2776225796 Nov 08, 2017 (151)
56 SWEGEN ss2989886826 Nov 08, 2017 (151)
57 ILLUMINA ss3021991756 Nov 08, 2017 (151)
58 BIOINF_KMB_FNS_UNIBA ss3024113094 Nov 08, 2017 (151)
59 TOPMED ss3314309494 Nov 08, 2017 (151)
60 CSHL ss3344335953 Nov 08, 2017 (151)
61 ILLUMINA ss3625760583 Oct 11, 2018 (152)
62 ILLUMINA ss3628114522 Oct 11, 2018 (152)
63 ILLUMINA ss3631609494 Oct 11, 2018 (152)
64 ILLUMINA ss3633208508 Oct 11, 2018 (152)
65 ILLUMINA ss3633920540 Oct 11, 2018 (152)
66 ILLUMINA ss3634776970 Oct 11, 2018 (152)
67 ILLUMINA ss3635606619 Oct 11, 2018 (152)
68 ILLUMINA ss3636464228 Oct 11, 2018 (152)
69 ILLUMINA ss3637358516 Oct 11, 2018 (152)
70 ILLUMINA ss3638273305 Oct 11, 2018 (152)
71 ILLUMINA ss3640484272 Oct 11, 2018 (152)
72 ILLUMINA ss3641109424 Oct 11, 2018 (152)
73 ILLUMINA ss3641405290 Oct 11, 2018 (152)
74 ILLUMINA ss3644748789 Oct 11, 2018 (152)
75 ILLUMINA ss3652427339 Oct 11, 2018 (152)
76 EGCUT_WGS ss3657875215 Jul 13, 2019 (153)
77 EVA_DECODE ss3704358101 Jul 13, 2019 (153)
78 ILLUMINA ss3725804122 Jul 13, 2019 (153)
79 ACPOP ss3728636146 Jul 13, 2019 (153)
80 ILLUMINA ss3744179110 Jul 13, 2019 (153)
81 ILLUMINA ss3745076862 Jul 13, 2019 (153)
82 EVA ss3757052151 Jul 13, 2019 (153)
83 ILLUMINA ss3772573626 Jul 13, 2019 (153)
84 KHV_HUMAN_GENOMES ss3801421558 Jul 13, 2019 (153)
85 EVA ss3827097724 Apr 25, 2020 (154)
86 SGDP_PRJ ss3852761823 Apr 25, 2020 (154)
87 KRGDB ss3898203413 Apr 25, 2020 (154)
88 KOGIC ss3948218802 Apr 25, 2020 (154)
89 1000Genomes NC_000002.11 - 85886013 Oct 11, 2018 (152)
90 The Avon Longitudinal Study of Parents and Children NC_000002.11 - 85886013 Oct 11, 2018 (152)
91 Chileans NC_000002.11 - 85886013 Apr 25, 2020 (154)
92 Genetic variation in the Estonian population NC_000002.11 - 85886013 Oct 11, 2018 (152)
93 The Danish reference pan genome NC_000002.11 - 85886013 Apr 25, 2020 (154)
94 gnomAD - Genomes NC_000002.11 - 85886013 Jul 13, 2019 (153)
95 Genome of the Netherlands Release 5 NC_000002.11 - 85886013 Apr 25, 2020 (154)
96 HapMap NC_000002.12 - 85658890 Apr 25, 2020 (154)
97 KOREAN population from KRGDB NC_000002.11 - 85886013 Apr 25, 2020 (154)
98 Korean Genome Project NC_000002.12 - 85658890 Apr 25, 2020 (154)
99 Northern Sweden NC_000002.11 - 85886013 Jul 13, 2019 (153)
100 Qatari NC_000002.11 - 85886013 Apr 25, 2020 (154)
101 SGDP_PRJ NC_000002.11 - 85886013 Apr 25, 2020 (154)
102 Siberian NC_000002.11 - 85886013 Apr 25, 2020 (154)
103 TopMed NC_000002.12 - 85658890 Oct 11, 2018 (152)
104 UK 10K study - Twins NC_000002.11 - 85886013 Oct 11, 2018 (152)
105 A Vietnamese Genetic Variation Database NC_000002.11 - 85886013 Jul 13, 2019 (153)
106 dbGaP Population Frequency Project NC_000002.12 - 85658890 Apr 25, 2020 (154)
Help

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Associated ID History Updated (Build)
rs1061246 Jan 18, 2001 (92)
rs3202292 Jul 03, 2002 (106)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
5380807, ss3898203413 NC_000002.11:85886012:T:A NC_000002.12:85658889:T:A
ss77328827 NC_000002.9:85797670:T:C NC_000002.12:85658889:T:C (self)
ss109698942, ss110594549, ss117791423, ss163719021, ss200735809, ss276557565, ss481543069, ss1586506190, ss1712473139 NC_000002.10:85739523:T:C NC_000002.12:85658889:T:C (self)
9184026, 5107086, 224033, 3613463, 5146654, 25059035, 2241080, 5380807, 1921011, 2359133, 4778803, 1254571, 5107086, 1109944, ss219376195, ss231262491, ss238795451, ss481572117, ss482545341, ss485566537, ss537463265, ss555718091, ss649311285, ss778972170, ss783228815, ss784183026, ss832489194, ss834434233, ss977083339, ss1069307062, ss1298205381, ss1428649411, ss1578978158, ss1604028660, ss1647022693, ss1752372905, ss1797089066, ss1920317203, ss1946046031, ss1958436749, ss1968827053, ss2020693313, ss2148738217, ss2398291606, ss2624854235, ss2633644191, ss2703317873, ss2710906460, ss2776225796, ss2989886826, ss3021991756, ss3344335953, ss3625760583, ss3628114522, ss3631609494, ss3633208508, ss3633920540, ss3634776970, ss3635606619, ss3636464228, ss3637358516, ss3638273305, ss3640484272, ss3641109424, ss3641405290, ss3644748789, ss3652427339, ss3657875215, ss3728636146, ss3744179110, ss3745076862, ss3757052151, ss3772573626, ss3827097724, ss3852761823, ss3898203413 NC_000002.11:85886012:T:C NC_000002.12:85658889:T:C (self)
1845819, 4596803, 198445647, 801889767, ss2232308925, ss3024113094, ss3314309494, ss3704358101, ss3725804122, ss3801421558, ss3948218802 NC_000002.12:85658889:T:C NC_000002.12:85658889:T:C (self)
ss9144, ss4116385, ss4250774, ss24789670, ss52088713, ss76754306, ss104807870, ss160872063, ss174337284 NT_022184.15:64707899:T:C NC_000002.12:85658889:T:C (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

4 citations for rs7316
PMID Title Author Year Journal
21283003 The influence of genetic variation in surfactant protein B on severe lung injury in African American children. Dahmer MK et al. 2011 Critical care medicine
28738720 Association of SP-B gene 9306 A/G polymorphism (rs7316) and risk of RDS. Fatahi N et al. 2018 The journal of maternal-fetal & neonatal medicine
30333828 Genetic Association of Pulmonary Surfactant Protein Genes, SFTPA1, SFTPA2, SFTPB, SFTPC, and SFTPD With Cystic Fibrosis. Lin Z et al. 2018 Frontiers in immunology
31016788 Gene polymorphisms of SFTPB rs7316, rs9752 and PAOX rs1046175 affect the diagnostic value of plasma Pro-SFTPB and DAS in Chinese Han non-small-cell lung cancer patients. Wang K et al. 2019 Journal of cellular biochemistry
Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

Genomic regions, transcripts, and products
Top Help

NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Software version is: 2.0.1.post565+e32b82c