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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.

rs541157948

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr3:129002068 (GRCh38.p14) 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
C>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.000011 (3/264690, TOPMED)
T=0.000007 (1/140202, GnomAD)
T=0.000219 (28/127950, GnomAD_exome) (+ 6 more)
T=0.00007 (1/14514, ALFA)
T=0.00077 (8/10412, ExAC)
T=0.0012 (8/6404, 1000G_30x)
T=0.0008 (4/5008, 1000G)
C=0.5 (1/2, SGDP_PRJ)
T=0.5 (1/2, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
EFCC1 : Missense Variant
CFAP92 : Intron Variant
Publications
0 citations
Genomic View
See rs on genome

ALFA Allele Frequency
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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 14514 C=0.99993 G=0.00000, T=0.00007
European Sub 9690 C=1.0000 G=0.0000, T=0.0000
African Sub 3312 C=0.9997 G=0.0000, T=0.0003
African Others Sub 114 C=1.000 G=0.000, T=0.000
African American Sub 3198 C=0.9997 G=0.0000, T=0.0003
Asian Sub 112 C=1.000 G=0.000, T=0.000
East Asian Sub 86 C=1.00 G=0.00, T=0.00
Other Asian Sub 26 C=1.00 G=0.00, T=0.00
Latin American 1 Sub 146 C=1.000 G=0.000, T=0.000
Latin American 2 Sub 610 C=1.000 G=0.000, T=0.000
South Asian Sub 98 C=1.00 G=0.00, T=0.00
Other Sub 546 C=1.000 G=0.000, T=0.000


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 264690 C=0.999989 G=0.000011
gnomAD - Genomes Global Study-wide 140202 C=0.999993 T=0.000007
gnomAD - Genomes European Sub 75922 C=0.99999 T=0.00001
gnomAD - Genomes African Sub 42010 C=1.00000 T=0.00000
gnomAD - Genomes American Sub 13664 C=1.00000 T=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3132 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2150 C=1.0000 T=0.0000
gnomAD - Exomes Global Study-wide 127950 C=0.999781 T=0.000219
gnomAD - Exomes European Sub 59382 C=1.00000 T=0.00000
gnomAD - Exomes Asian Sub 29906 C=0.99906 T=0.00094
gnomAD - Exomes American Sub 23062 C=1.00000 T=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 7690 C=1.0000 T=0.0000
gnomAD - Exomes African Sub 4158 C=1.0000 T=0.0000
gnomAD - Exomes Other Sub 3752 C=1.0000 T=0.0000
Allele Frequency Aggregator Total Global 14514 C=0.99993 G=0.00000, T=0.00007
Allele Frequency Aggregator European Sub 9690 C=1.0000 G=0.0000, T=0.0000
Allele Frequency Aggregator African Sub 3312 C=0.9997 G=0.0000, T=0.0003
Allele Frequency Aggregator Latin American 2 Sub 610 C=1.000 G=0.000, T=0.000
Allele Frequency Aggregator Other Sub 546 C=1.000 G=0.000, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 C=1.000 G=0.000, T=0.000
Allele Frequency Aggregator Asian Sub 112 C=1.000 G=0.000, T=0.000
Allele Frequency Aggregator South Asian Sub 98 C=1.00 G=0.00, T=0.00
ExAC Global Study-wide 10412 C=0.99923 T=0.00077
ExAC Asian Sub 7130 C=0.9989 T=0.0011
ExAC Europe Sub 2778 C=1.0000 T=0.0000
ExAC African Sub 288 C=1.000 T=0.000
ExAC Other Sub 116 C=1.000 T=0.000
ExAC American Sub 100 C=1.00 T=0.00
1000Genomes_30x Global Study-wide 6404 C=0.9988 T=0.0012
1000Genomes_30x African Sub 1786 C=1.0000 T=0.0000
1000Genomes_30x Europe Sub 1266 C=1.0000 T=0.0000
1000Genomes_30x South Asian Sub 1202 C=0.9933 T=0.0067
1000Genomes_30x East Asian Sub 1170 C=1.0000 T=0.0000
1000Genomes_30x American Sub 980 C=1.000 T=0.000
1000Genomes Global Study-wide 5008 C=0.9992 T=0.0008
1000Genomes African Sub 1322 C=1.0000 T=0.0000
1000Genomes East Asian Sub 1008 C=1.0000 T=0.0000
1000Genomes Europe Sub 1006 C=1.0000 T=0.0000
1000Genomes South Asian Sub 978 C=0.996 T=0.004
1000Genomes American Sub 694 C=1.000 T=0.000
SGDP_PRJ Global Study-wide 2 C=0.5 T=0.5
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.p14 chr 3 NC_000003.12:g.129002068C>G
GRCh38.p14 chr 3 NC_000003.12:g.129002068C>T
GRCh37.p13 chr 3 NC_000003.11:g.128720911C>G
GRCh37.p13 chr 3 NC_000003.11:g.128720911C>T
Gene: CFAP92, cilia and flagella associated protein 92 (putative) (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CFAP92 transcript variant 2 NM_001348521.2:c.-814+169…

NM_001348521.2:c.-814+1697G>C

N/A Intron Variant
CFAP92 transcript variant 1 NM_001348520.2:c.-537= N/A 5 Prime UTR Variant
CFAP92 transcript variant 4 NM_001348522.2:c. N/A Genic Upstream Transcript Variant
CFAP92 transcript variant 5 NM_001348523.2:c. N/A Genic Upstream Transcript Variant
CFAP92 transcript variant 6 NM_001394090.1:c. N/A Genic Upstream Transcript Variant
CFAP92 transcript variant 3 NM_020741.3:c. N/A Genic Upstream Transcript Variant
CFAP92 transcript variant X2 XM_011513050.3:c.65-8732G…

XM_011513050.3:c.65-8732G>C

N/A Intron Variant
CFAP92 transcript variant X3 XM_017006945.2:c.65-8732G…

XM_017006945.2:c.65-8732G>C

N/A Intron Variant
CFAP92 transcript variant X1 XM_047448637.1:c.65-8732G…

XM_047448637.1:c.65-8732G>C

N/A Intron Variant
CFAP92 transcript variant X4 XM_047448638.1:c.65-8732G…

XM_047448638.1:c.65-8732G>C

N/A Intron Variant
CFAP92 transcript variant X5 XM_047448639.1:c.65-8732G…

XM_047448639.1:c.65-8732G>C

N/A Intron Variant
CFAP92 transcript variant X6 XM_047448640.1:c. N/A Genic Upstream Transcript Variant
Gene: EFCC1, EF-hand and coiled-coil domain containing 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
EFCC1 transcript variant 1 NM_001377500.1:c.440C>G A [GCG] > G [GGG] Coding Sequence Variant
EF-hand and coiled-coil domain-containing protein 1 isoform 1 NP_001364429.1:p.Ala147Gly A (Ala) > G (Gly) Missense Variant
EFCC1 transcript variant 1 NM_001377500.1:c.440C>T A [GCG] > V [GTG] Coding Sequence Variant
EF-hand and coiled-coil domain-containing protein 1 isoform 1 NP_001364429.1:p.Ala147Val A (Ala) > V (Val) Missense Variant
EFCC1 transcript variant 3 NM_001377501.1:c.440C>G A [GCG] > G [GGG] Coding Sequence Variant
EF-hand and coiled-coil domain-containing protein 1 isoform 3 NP_001364430.1:p.Ala147Gly A (Ala) > G (Gly) Missense Variant
EFCC1 transcript variant 3 NM_001377501.1:c.440C>T A [GCG] > V [GTG] Coding Sequence Variant
EF-hand and coiled-coil domain-containing protein 1 isoform 3 NP_001364430.1:p.Ala147Val A (Ala) > V (Val) Missense Variant
EFCC1 transcript variant 2 NM_024768.3:c.440C>G A [GCG] > G [GGG] Coding Sequence Variant
EF-hand and coiled-coil domain-containing protein 1 isoform 2 NP_079044.2:p.Ala147Gly A (Ala) > G (Gly) Missense Variant
EFCC1 transcript variant 2 NM_024768.3:c.440C>T A [GCG] > V [GTG] Coding Sequence Variant
EF-hand and coiled-coil domain-containing protein 1 isoform 2 NP_079044.2:p.Ala147Val A (Ala) > V (Val) Missense Variant
EFCC1 transcript variant X1 XM_011513161.3:c. N/A Genic Upstream Transcript Variant
EFCC1 transcript variant X6 XM_011513164.3:c. N/A Genic Upstream Transcript Variant
EFCC1 transcript variant X4 XM_047448963.1:c.440C>G A [GCG] > G [GGG] Coding Sequence Variant
EF-hand and coiled-coil domain-containing protein 1 isoform X2 XP_047304919.1:p.Ala147Gly A (Ala) > G (Gly) Missense Variant
EFCC1 transcript variant X4 XM_047448963.1:c.440C>T A [GCG] > V [GTG] Coding Sequence Variant
EF-hand and coiled-coil domain-containing protein 1 isoform X2 XP_047304919.1:p.Ala147Val A (Ala) > V (Val) Missense Variant
EFCC1 transcript variant X5 XM_011513163.4:c.440C>G A [GCG] > G [GGG] Coding Sequence Variant
EF-hand and coiled-coil domain-containing protein 1 isoform X3 XP_011511465.1:p.Ala147Gly A (Ala) > G (Gly) Missense Variant
EFCC1 transcript variant X5 XM_011513163.4:c.440C>T A [GCG] > V [GTG] Coding Sequence Variant
EF-hand and coiled-coil domain-containing protein 1 isoform X3 XP_011511465.1:p.Ala147Val A (Ala) > V (Val) Missense Variant
EFCC1 transcript variant X2 XR_007095727.1:n.765C>G N/A Non Coding Transcript Variant
EFCC1 transcript variant X2 XR_007095727.1:n.765C>T N/A Non Coding Transcript Variant
EFCC1 transcript variant X3 XR_924178.4:n.765C>G N/A Non Coding Transcript Variant
EFCC1 transcript variant X3 XR_924178.4:n.765C>T N/A Non Coding 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

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 C= G T
GRCh38.p14 chr 3 NC_000003.12:g.129002068= NC_000003.12:g.129002068C>G NC_000003.12:g.129002068C>T
GRCh37.p13 chr 3 NC_000003.11:g.128720911= NC_000003.11:g.128720911C>G NC_000003.11:g.128720911C>T
EFCC1 transcript variant X3 XR_924178.4:n.765= XR_924178.4:n.765C>G XR_924178.4:n.765C>T
EFCC1 transcript variant X3 XR_924178.3:n.524= XR_924178.3:n.524C>G XR_924178.3:n.524C>T
EFCC1 transcript variant X3 XR_924178.2:n.465= XR_924178.2:n.465C>G XR_924178.2:n.465C>T
EFCC1 transcript variant X3 XR_924178.1:n.818= XR_924178.1:n.818C>G XR_924178.1:n.818C>T
EFCC1 transcript variant X5 XM_011513163.4:c.440= XM_011513163.4:c.440C>G XM_011513163.4:c.440C>T
EFCC1 transcript variant X5 XM_011513163.3:c.440= XM_011513163.3:c.440C>G XM_011513163.3:c.440C>T
EFCC1 transcript variant X5 XM_011513163.2:c.440= XM_011513163.2:c.440C>G XM_011513163.2:c.440C>T
EFCC1 transcript variant X5 XM_011513163.1:c.440= XM_011513163.1:c.440C>G XM_011513163.1:c.440C>T
EFCC1 transcript variant 2 NM_024768.3:c.440= NM_024768.3:c.440C>G NM_024768.3:c.440C>T
EFCC1 transcript NM_024768.2:c.440= NM_024768.2:c.440C>G NM_024768.2:c.440C>T
CFAP92 transcript variant 1 NM_001348520.2:c.-537= NM_001348520.2:c.-537G>C NM_001348520.2:c.-537G>A
KIAA1257 transcript variant 1 NM_001348520.1:c.-537= NM_001348520.1:c.-537G>C NM_001348520.1:c.-537G>A
EFCC1 transcript variant X2 XR_007095727.1:n.765= XR_007095727.1:n.765C>G XR_007095727.1:n.765C>T
EFCC1 transcript variant 1 NM_001377500.1:c.440= NM_001377500.1:c.440C>G NM_001377500.1:c.440C>T
EFCC1 transcript variant 3 NM_001377501.1:c.440= NM_001377501.1:c.440C>G NM_001377501.1:c.440C>T
EFCC1 transcript variant X4 XM_047448963.1:c.440= XM_047448963.1:c.440C>G XM_047448963.1:c.440C>T
EF-hand and coiled-coil domain-containing protein 1 isoform X3 XP_011511465.1:p.Ala147= XP_011511465.1:p.Ala147Gly XP_011511465.1:p.Ala147Val
EF-hand and coiled-coil domain-containing protein 1 isoform 2 NP_079044.2:p.Ala147= NP_079044.2:p.Ala147Gly NP_079044.2:p.Ala147Val
EF-hand and coiled-coil domain-containing protein 1 isoform 1 NP_001364429.1:p.Ala147= NP_001364429.1:p.Ala147Gly NP_001364429.1:p.Ala147Val
EF-hand and coiled-coil domain-containing protein 1 isoform 3 NP_001364430.1:p.Ala147= NP_001364430.1:p.Ala147Gly NP_001364430.1:p.Ala147Val
EF-hand and coiled-coil domain-containing protein 1 isoform X2 XP_047304919.1:p.Ala147= XP_047304919.1:p.Ala147Gly XP_047304919.1:p.Ala147Val
CFAP92 transcript variant 2 NM_001348521.2:c.-814+1697= NM_001348521.2:c.-814+1697G>C NM_001348521.2:c.-814+1697G>A
CFAP92 transcript variant X2 XM_011513050.3:c.65-8732= XM_011513050.3:c.65-8732G>C XM_011513050.3:c.65-8732G>A
CFAP92 transcript variant X3 XM_017006945.2:c.65-8732= XM_017006945.2:c.65-8732G>C XM_017006945.2:c.65-8732G>A
CFAP92 transcript variant X1 XM_047448637.1:c.65-8732= XM_047448637.1:c.65-8732G>C XM_047448637.1:c.65-8732G>A
CFAP92 transcript variant X4 XM_047448638.1:c.65-8732= XM_047448638.1:c.65-8732G>C XM_047448638.1:c.65-8732G>A
CFAP92 transcript variant X5 XM_047448639.1:c.65-8732= XM_047448639.1:c.65-8732G>C XM_047448639.1:c.65-8732G>A
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#.

12 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss1306099377 Aug 21, 2014 (142)
2 EVA_EXAC ss1687199448 Apr 01, 2015 (144)
3 GNOMAD ss2734053622 Nov 08, 2017 (151)
4 GNOMAD ss2747096681 Nov 08, 2017 (151)
5 GNOMAD ss2798960609 Nov 08, 2017 (151)
6 ILLUMINA ss3726055764 Jul 13, 2019 (153)
7 SGDP_PRJ ss3856938814 Apr 25, 2020 (154)
8 TOPMED ss4583142232 Apr 26, 2021 (155)
9 1000G_HIGH_COVERAGE ss5255976952 Oct 12, 2022 (156)
10 EVA ss5343176126 Oct 12, 2022 (156)
11 1000G_HIGH_COVERAGE ss5535390857 Oct 12, 2022 (156)
12 EVA ss5870946061 Oct 12, 2022 (156)
13 1000Genomes NC_000003.11 - 128720911 Oct 12, 2018 (152)
14 1000Genomes_30x NC_000003.12 - 129002068 Oct 12, 2022 (156)
15 ExAC NC_000003.11 - 128720911 Oct 12, 2018 (152)
16 gnomAD - Genomes NC_000003.12 - 129002068 Apr 26, 2021 (155)
17 gnomAD - Exomes NC_000003.11 - 128720911 Jul 13, 2019 (153)
18 SGDP_PRJ NC_000003.11 - 128720911 Apr 25, 2020 (154)
19 TopMed NC_000003.12 - 129002068 Apr 26, 2021 (155)
20 ALFA NC_000003.12 - 129002068 Apr 26, 2021 (155)
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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
420519787, 527143321, ss4583142232 NC_000003.12:129002067:C:G NC_000003.12:129002067:C:G (self)
17359991, 7138274, 3141221, 8955794, ss1306099377, ss1687199448, ss2734053622, ss2747096681, ss2798960609, ss3856938814, ss5343176126 NC_000003.11:128720910:C:T NC_000003.12:129002067:C:T (self)
22916792, 123384420, 527143321, ss3726055764, ss5255976952, ss5535390857, ss5870946061 NC_000003.12:129002067:C:T NC_000003.12:129002067:C:T (self)
Help

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

No publications for rs541157948

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.post761+d5e8e07