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dbSNP Short Genetic Variations

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 152

Released October 2, 2018

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>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.14913 (18726/125568, TOPMED)
C=0.1371 (4239/30918, GnomAD)
C=0.177 (886/5008, 1000G) (+ 3 more)
C=0.085 (379/4480, Estonian)
C=0.072 (277/3854, ALSPAC)
C=0.080 (295/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SFTPB : Intron Variant
Publications
2 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>C
GRCh37.p13 chr 2 NC_000002.11:g.85886013T>C
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 2 NM_198843.2:c. N/A Intron Variant
SFTPB transcript variant 1 NM_000542.3:c. N/A 3 Prime UTR Variant
SFTPB transcript variant X1 XM_005264487.2:c. N/A 3 Prime UTR Variant
SFTPB transcript variant X2 XM_005264488.4:c. 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
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=0.85087 C=0.14913
gnomAD - Genomes Global Study-wide 30918 T=0.8629 C=0.1371
gnomAD - Genomes European Sub 18484 T=0.9227 C=0.0773
gnomAD - Genomes African Sub 8702 T=0.758 C=0.242
gnomAD - Genomes East Asian Sub 1614 T=0.752 C=0.248
gnomAD - Genomes Other Sub 982 T=0.90 C=0.10
gnomAD - Genomes American Sub 834 T=0.78 C=0.22
gnomAD - Genomes Ashkenazi Jewish Sub 302 T=0.93 C=0.07
1000Genomes Global Study-wide 5008 T=0.823 C=0.177
1000Genomes African Sub 1322 T=0.737 C=0.263
1000Genomes East Asian Sub 1008 T=0.778 C=0.222
1000Genomes Europe Sub 1006 T=0.896 C=0.104
1000Genomes South Asian Sub 978 T=0.93 C=0.07
1000Genomes American Sub 694 T=0.79 C=0.21
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.915 C=0.085
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.928 C=0.072
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.920 C=0.080
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= C Note
GRCh38.p12 chr 2 NC_000002.12:g.85658890T= NC_000002.12:g.85658890T>C
GRCh37.p13 chr 2 NC_000002.11:g.85886013T= NC_000002.11:g.85886013T>C
SFTPB RefSeqGene NG_016967.1:g.14852A= NG_016967.1:g.14852A>G
SFTPB transcript variant 1 NM_000542.3:c.*812A= NM_000542.3:c.*812A>G
SFTPB transcript variant X2 XM_005264488.4:c.*812A= XM_005264488.4:c.*812A>G
SFTPB transcript variant X2 XM_005264488.1:c.*812A= XM_005264488.1:c.*812A>G
SFTPB transcript variant X1 XM_005264487.2:c.*856A= XM_005264487.2:c.*856A>G
SFTPB transcript variant X1 XM_005264487.1:c.*856A= XM_005264487.1:c.*856A>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#.

77 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 CGAP-GAI ss9144 Sep 19, 2000 (52)
2 LEE ss1545977 Oct 05, 2000 (92)
3 SC_JCM ss4116385 Nov 05, 2001 (101)
4 PGA-UW-FHCRC ss4250774 Jan 04, 2002 (102)
5 LEE ss4431470 May 29, 2002 (106)
6 SEQUENOM ss24789670 Sep 20, 2004 (123)
7 PGA-UW-FHCRC ss52088713 Oct 16, 2006 (127)
8 AFFY ss76754306 Dec 07, 2007 (129)
9 HGSV ss77328827 Dec 07, 2007 (129)
10 KRIBB_YJKIM ss104807870 Feb 05, 2009 (130)
11 1000GENOMES ss109698942 Jan 24, 2009 (130)
12 1000GENOMES ss110594549 Jan 25, 2009 (130)
13 ILLUMINA-UK ss117791423 Feb 14, 2009 (130)
14 ILLUMINA ss160872063 Dec 01, 2009 (131)
15 COMPLETE_GENOMICS ss163719021 Jul 04, 2010 (132)
16 ILLUMINA ss174337284 Jul 04, 2010 (132)
17 BUSHMAN ss200735809 Jul 04, 2010 (132)
18 1000GENOMES ss219376195 Jul 14, 2010 (132)
19 1000GENOMES ss231262491 Jul 14, 2010 (132)
20 1000GENOMES ss238795451 Jul 15, 2010 (132)
21 GMI ss276557565 May 04, 2012 (137)
22 ILLUMINA ss481543069 May 04, 2012 (137)
23 ILLUMINA ss481572117 May 04, 2012 (137)
24 ILLUMINA ss482545341 Sep 08, 2015 (146)
25 ILLUMINA ss485566537 May 04, 2012 (137)
26 ILLUMINA ss537463265 Sep 08, 2015 (146)
27 TISHKOFF ss555718091 Apr 25, 2013 (138)
28 SSMP ss649311285 Apr 25, 2013 (138)
29 ILLUMINA ss778972170 Sep 08, 2015 (146)
30 ILLUMINA ss783228815 Sep 08, 2015 (146)
31 ILLUMINA ss784183026 Sep 08, 2015 (146)
32 ILLUMINA ss832489194 Sep 08, 2015 (146)
33 ILLUMINA ss834434233 Sep 08, 2015 (146)
34 EVA-GONL ss977083339 Aug 21, 2014 (142)
35 JMKIDD_LAB ss1069307062 Aug 21, 2014 (142)
36 1000GENOMES ss1298205381 Aug 21, 2014 (142)
37 DDI ss1428649411 Apr 01, 2015 (144)
38 EVA_GENOME_DK ss1578978158 Apr 01, 2015 (144)
39 EVA_DECODE ss1586506190 Apr 01, 2015 (144)
40 EVA_UK10K_ALSPAC ss1604028660 Apr 01, 2015 (144)
41 EVA_UK10K_TWINSUK ss1647022693 Apr 01, 2015 (144)
42 EVA_SVP ss1712473139 Apr 01, 2015 (144)
43 ILLUMINA ss1752372905 Sep 08, 2015 (146)
44 HAMMER_LAB ss1797089066 Sep 08, 2015 (146)
45 WEILL_CORNELL_DGM ss1920317203 Feb 12, 2016 (147)
46 ILLUMINA ss1946046031 Feb 12, 2016 (147)
47 ILLUMINA ss1958436749 Feb 12, 2016 (147)
48 GENOMED ss1968827053 Jul 19, 2016 (147)
49 JJLAB ss2020693313 Sep 14, 2016 (149)
50 USC_VALOUEV ss2148738217 Dec 20, 2016 (150)
51 HUMAN_LONGEVITY ss2232308925 Dec 20, 2016 (150)
52 TOPMED ss2398291606 Dec 20, 2016 (150)
53 SYSTEMSBIOZJU ss2624854235 Nov 08, 2017 (151)
54 ILLUMINA ss2633644191 Nov 08, 2017 (151)
55 GRF ss2703317873 Nov 08, 2017 (151)
56 ILLUMINA ss2710906460 Nov 08, 2017 (151)
57 GNOMAD ss2776225796 Nov 08, 2017 (151)
58 SWEGEN ss2989886826 Nov 08, 2017 (151)
59 ILLUMINA ss3021991756 Nov 08, 2017 (151)
60 BIOINF_KMB_FNS_UNIBA ss3024113094 Nov 08, 2017 (151)
61 TOPMED ss3314309494 Nov 08, 2017 (151)
62 CSHL ss3344335953 Nov 08, 2017 (151)
63 ILLUMINA ss3625760583 Oct 11, 2018 (152)
64 ILLUMINA ss3628114522 Oct 11, 2018 (152)
65 ILLUMINA ss3631609494 Oct 11, 2018 (152)
66 ILLUMINA ss3633208508 Oct 11, 2018 (152)
67 ILLUMINA ss3633920540 Oct 11, 2018 (152)
68 ILLUMINA ss3634776970 Oct 11, 2018 (152)
69 ILLUMINA ss3635606619 Oct 11, 2018 (152)
70 ILLUMINA ss3636464228 Oct 11, 2018 (152)
71 ILLUMINA ss3637358516 Oct 11, 2018 (152)
72 ILLUMINA ss3638273305 Oct 11, 2018 (152)
73 ILLUMINA ss3640484272 Oct 11, 2018 (152)
74 ILLUMINA ss3641109424 Oct 11, 2018 (152)
75 ILLUMINA ss3641405290 Oct 11, 2018 (152)
76 ILLUMINA ss3644748789 Oct 11, 2018 (152)
77 ILLUMINA ss3652427339 Oct 11, 2018 (152)
78 1000Genomes NC_000002.11 - 85886013 Oct 11, 2018 (152)
79 The Avon Longitudinal Study of Parents and Children NC_000002.11 - 85886013 Oct 11, 2018 (152)
80 Genetic variation in the Estonian population NC_000002.11 - 85886013 Oct 11, 2018 (152)
81 gnomAD - Genomes NC_000002.11 - 85886013 Oct 11, 2018 (152)
82 TopMed NC_000002.12 - 85658890 Oct 11, 2018 (152)
83 UK 10K study - Twins NC_000002.11 - 85886013 Oct 11, 2018 (152)
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
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, 3613463, 105715657, 5107086, 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 NC_000002.11:85886012:T:C NC_000002.12:85658889:T:C (self)
198445647, ss2232308925, ss3024113094, ss3314309494 NC_000002.12:85658889:T:C NC_000002.12:85658889:T:C (self)
ss9144, ss1545977, ss4116385, ss4250774, ss4431470, 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.

2 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

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.post104+4a6ee9c