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dbSNP Short Genetic Variations

Reference SNP (rs) Report

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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.

rs28942091

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr3:9943452 (GRCh38.p7) 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
T=0.00067 (164/246212, GnomAD)
T=0.00089 (112/125568, TOPMED)
T=0.00064 (77/121162, ExAC) (+ 4 more)
T=0.0007 (22/30870, GnomAD)
T=0.001 (4/5008, 1000G)
T=0.001 (2/3854, ALSPAC)
T=0.001 (2/3708, TWINSUK)
Clinical Significance
Reported in ClinVar
Gene : Consequence
CRELD1 : Missense Variant
Publications
5 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.p7 chr 3 NC_000003.12:g.9943452C>G
GRCh38.p7 chr 3 NC_000003.12:g.9943452C>T
GRCh37.p13 chr 3 NC_000003.11:g.9985136C>G
GRCh37.p13 chr 3 NC_000003.11:g.9985136C>T
CRELD1 RefSeqGene NG_017069.1:g.14612C>G
CRELD1 RefSeqGene NG_017069.1:g.14612C>T
Gene: CRELD1, cysteine rich with EGF like domains 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CRELD1 transcript variant 2 NM_015513.4:c.985C>G R [CGC] > G [GGC] Coding Sequence Variant
cysteine-rich with EGF-like domain protein 1 isoform 2 precursor NP_056328.2:p.Arg...

NP_056328.2:p.Arg329Gly

R (Arg) > G (Gly) Missense Variant
CRELD1 transcript variant 2 NM_015513.4:c.985C>T R [CGC] > C [TGC] Coding Sequence Variant
cysteine-rich with EGF-like domain protein 1 isoform 2 precursor NP_056328.2:p.Arg...

NP_056328.2:p.Arg329Cys

R (Arg) > C (Cys) Missense Variant
CRELD1 transcript variant 1 NM_001031717.3:c....

NM_001031717.3:c.985C>G

R [CGC] > G [GGC] Coding Sequence Variant
cysteine-rich with EGF-like domain protein 1 isoform 1 precursor NP_001026887.1:p....

NP_001026887.1:p.Arg329Gly

R (Arg) > G (Gly) Missense Variant
CRELD1 transcript variant 1 NM_001031717.3:c....

NM_001031717.3:c.985C>T

R [CGC] > C [TGC] Coding Sequence Variant
cysteine-rich with EGF-like domain protein 1 isoform 1 precursor NP_001026887.1:p....

NP_001026887.1:p.Arg329Cys

R (Arg) > C (Cys) Missense Variant
CRELD1 transcript variant 3 NM_001077415.2:c....

NM_001077415.2:c.985C>G

R [CGC] > G [GGC] Coding Sequence Variant
cysteine-rich with EGF-like domain protein 1 isoform 2 precursor NP_001070883.1:p....

NP_001070883.1:p.Arg329Gly

R (Arg) > G (Gly) Missense Variant
CRELD1 transcript variant 3 NM_001077415.2:c....

NM_001077415.2:c.985C>T

R [CGC] > C [TGC] Coding Sequence Variant
cysteine-rich with EGF-like domain protein 1 isoform 2 precursor NP_001070883.1:p....

NP_001070883.1:p.Arg329Cys

R (Arg) > C (Cys) Missense Variant
CRELD1 transcript variant X1 XM_011534108.1:c....

XM_011534108.1:c.985C>G

R [CGC] > G [GGC] Coding Sequence Variant
cysteine-rich with EGF-like domain protein 1 isoform X1 XP_011532410.1:p....

XP_011532410.1:p.Arg329Gly

R (Arg) > G (Gly) Missense Variant
CRELD1 transcript variant X1 XM_011534108.1:c....

XM_011534108.1:c.985C>T

R [CGC] > C [TGC] Coding Sequence Variant
cysteine-rich with EGF-like domain protein 1 isoform X1 XP_011532410.1:p....

XP_011532410.1:p.Arg329Cys

R (Arg) > C (Cys) Missense Variant
CRELD1 transcript variant X2 XM_017007175.1:c....

XM_017007175.1:c.985C>G

R [CGC] > G [GGC] Coding Sequence Variant
cysteine-rich with EGF-like domain protein 1 isoform X2 XP_016862664.1:p....

XP_016862664.1:p.Arg329Gly

R (Arg) > G (Gly) Missense Variant
CRELD1 transcript variant X2 XM_017007175.1:c....

XM_017007175.1:c.985C>T

R [CGC] > C [TGC] Coding Sequence Variant
cysteine-rich with EGF-like domain protein 1 isoform X2 XP_016862664.1:p....

XP_016862664.1:p.Arg329Cys

R (Arg) > C (Cys) Missense 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.

Allele: T (allele ID: 18466 )
ClinVar Accession Disease Names Clinical Significance
RCV000003596.4 Atrioventricular septal defect 2 Likely-Benign
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").

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Study Population Group Sample Size Ref Allele Alt Allele
The Genome Aggregation Database Global Study-wide 246212 C=0.99933 T=0.00067
The Genome Aggregation Database European Sub 133966 C=0.99904 T=0.00096
The Genome Aggregation Database Asian Sub 48030 C=1.0000 T=0.0000
The Genome Aggregation Database American Sub 33582 C=0.9994 T=0.0006
The Genome Aggregation Database African Sub 15298 C=0.9996 T=0.0004
The Genome Aggregation Database Ashkenazi Jewish Sub 9850 C=1.000 T=0.000
The Genome Aggregation Database Other Sub 5486 C=0.999 T=0.001
Trans-Omics for Precision Medicine Global Study-wide 125568 C=0.99910 G=0.00001, T=0.00089
The Exome Aggregation Consortium Global Study-wide 121162 C=0.99936 T=0.00064
The Exome Aggregation Consortium Europe Sub 73172 C=0.9991 T=0.0009
The Exome Aggregation Consortium Asian Sub 25152 C=0.9999 T=0.0001
The Exome Aggregation Consortium American Sub 11572 C=0.9997 T=0.0003
The Exome Aggregation Consortium African Sub 10364 C=0.9995 T=0.0005
The Exome Aggregation Consortium Other Sub 902 C=1.00 T=0.00
The Genome Aggregation Database Global Study-wide 30870 C=0.9993 T=0.0007
The Genome Aggregation Database European Sub 18422 C=0.9991 T=0.0009
The Genome Aggregation Database African Sub 8712 C=1.000 T=0.000
The Genome Aggregation Database East Asian Sub 1614 C=1.000 T=0.000
The Genome Aggregation Database Other Sub 982 C=1.00 T=0.00
The Genome Aggregation Database American Sub 838 C=1.00 T=0.00
The Genome Aggregation Database Ashkenazi Jewish Sub 302 C=1.00 T=0.00
1000Genomes Global Study-wide 5008 C=0.999 T=0.001
1000Genomes African Sub 1322 C=0.999 T=0.001
1000Genomes East Asian Sub 1008 C=1.000 T=0.000
1000Genomes Europe Sub 1006 C=0.998 T=0.002
1000Genomes South Asian Sub 978 C=1.00 T=0.00
1000Genomes American Sub 694 C=1.00 T=0.00
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.999 T=0.001
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.999 T=0.001
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 Note
GRCh38.p7 chr 3 NC_000003.12:g.99...

NC_000003.12:g.9943452C=

NC_000003.12:g.99...

NC_000003.12:g.9943452C>G

NC_000003.12:g.99...

NC_000003.12:g.9943452C>T

GRCh37.p13 chr 3 NC_000003.11:g.99...

NC_000003.11:g.9985136C=

NC_000003.11:g.99...

NC_000003.11:g.9985136C>G

NC_000003.11:g.99...

NC_000003.11:g.9985136C>T

CRELD1 RefSeqGene NG_017069.1:g.146...

NG_017069.1:g.14612C=

NG_017069.1:g.146...

NG_017069.1:g.14612C>G

NG_017069.1:g.146...

NG_017069.1:g.14612C>T

CRELD1 transcript variant 2 NM_015513.4:c.985C= NM_015513.4:c.985C>G NM_015513.4:c.985C>T
CRELD1 transcript variant 1 NM_001031717.3:c....

NM_001031717.3:c.985C=

NM_001031717.3:c....

NM_001031717.3:c.985C>G

NM_001031717.3:c....

NM_001031717.3:c.985C>T

CRELD1 transcript variant 3 NM_001077415.2:c....

NM_001077415.2:c.985C=

NM_001077415.2:c....

NM_001077415.2:c.985C>G

NM_001077415.2:c....

NM_001077415.2:c.985C>T

CRELD1 transcript variant X1 XM_011534108.1:c....

XM_011534108.1:c.985C=

XM_011534108.1:c....

XM_011534108.1:c.985C>G

XM_011534108.1:c....

XM_011534108.1:c.985C>T

CRELD1 transcript variant X2 XM_017007175.1:c....

XM_017007175.1:c.985C=

XM_017007175.1:c....

XM_017007175.1:c.985C>G

XM_017007175.1:c....

XM_017007175.1:c.985C>T

cysteine-rich with EGF-like domain protein 1 isoform 2 precursor NP_056328.2:p.Arg...

NP_056328.2:p.Arg329=

NP_056328.2:p.Arg...

NP_056328.2:p.Arg329Gly

NP_056328.2:p.Arg...

NP_056328.2:p.Arg329Cys

cysteine-rich with EGF-like domain protein 1 isoform 1 precursor NP_001026887.1:p....

NP_001026887.1:p.Arg329=

NP_001026887.1:p....

NP_001026887.1:p.Arg329Gly

NP_001026887.1:p....

NP_001026887.1:p.Arg329Cys

cysteine-rich with EGF-like domain protein 1 isoform 2 precursor NP_001070883.1:p....

NP_001070883.1:p.Arg329=

NP_001070883.1:p....

NP_001070883.1:p.Arg329Gly

NP_001070883.1:p....

NP_001070883.1:p.Arg329Cys

cysteine-rich with EGF-like domain protein 1 isoform X1 XP_011532410.1:p....

XP_011532410.1:p.Arg329=

XP_011532410.1:p....

XP_011532410.1:p.Arg329Gly

XP_011532410.1:p....

XP_011532410.1:p.Arg329Cys

cysteine-rich with EGF-like domain protein 1 isoform X2 XP_016862664.1:p....

XP_016862664.1:p.Arg329=

XP_016862664.1:p....

XP_016862664.1:p.Arg329Gly

XP_016862664.1:p....

XP_016862664.1:p.Arg329Cys

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#.

33 SubSNP, 1 ClinVar, 7 Frequency submissions
No Submitter Submission ID Date (Build)
1 OMIM-CURATED-RECORDS ss275513751 Nov 22, 2010 (133)
2 OMICIA ss275516287 Nov 30, 2010 (133)
3 NHLBI-ESP ss342113199 May 09, 2011 (134)
4 1000GENOMES ss488747055 May 04, 2012 (137)
5 EXOME_CHIP ss491335442 May 04, 2012 (137)
6 ILLUMINA ss780813362 Sep 08, 2015 (146)
7 ILLUMINA ss783495410 Sep 08, 2015 (146)
8 EVA-GONL ss978261287 Aug 21, 2014 (142)
9 1000GENOMES ss1302761109 Aug 21, 2014 (142)
10 EVA_FINRISK ss1584025775 Apr 01, 2015 (144)
11 EVA_DECODE ss1587721909 Apr 01, 2015 (144)
12 EVA_UK10K_ALSPAC ss1606392163 Apr 01, 2015 (144)
13 EVA_UK10K_TWINSUK ss1649386196 Apr 01, 2015 (144)
14 EVA_EXAC ss1686863563 Apr 01, 2015 (144)
15 EVA_MGP ss1711006722 Apr 01, 2015 (144)
16 ILLUMINA ss1752488956 Sep 08, 2015 (146)
17 ILLUMINA ss1917763169 Feb 12, 2016 (147)
18 ILLUMINA ss1946074244 Feb 12, 2016 (147)
19 ILLUMINA ss1958536051 Feb 12, 2016 (147)
20 HUMAN_LONGEVITY ss2248995598 Dec 20, 2016 (150)
21 TOPMED ss2416033479 Dec 20, 2016 (150)
22 GNOMAD ss2733532566 Nov 08, 2017 (151)
23 GNOMAD ss2746943291 Nov 08, 2017 (151)
24 GNOMAD ss2789416425 Nov 08, 2017 (151)
25 AFFY ss2985246651 Nov 08, 2017 (151)
26 SWEGEN ss2991812945 Nov 08, 2017 (151)
27 ILLUMINA ss3022210371 Nov 08, 2017 (151)
28 TOPMED ss3382405834 Nov 08, 2017 (151)
29 TOPMED ss3382405835 Nov 08, 2017 (151)
30 ILLUMINA ss3628587466 Jul 19, 2018 (151)
31 ILLUMINA ss3634879628 Jul 19, 2018 (151)
32 ILLUMINA ss3640586931 Jul 19, 2018 (151)
33 ILLUMINA ss3644806794 Jul 19, 2018 (151)
34 1000Genomes NC_000003.11 - 9985136 Jul 19, 2018 (151)
35 The Avon Longitudinal Study of Parents and Children NC_000003.11 - 9985136 Jul 19, 2018 (151)
36 The Exome Aggregation Consortium NC_000003.11 - 9985136 Jul 19, 2018 (151)
37 The Genome Aggregation Database NC_000003.11 - 9985136 Jul 19, 2018 (151)
38 The Genome Aggregation Database NC_000003.11 - 9985136 Jul 19, 2018 (151)
39 Trans-Omics for Precision Medicine NC_000003.12 - 9943452 Jul 19, 2018 (151)
40 UK 10K study - Twins NC_000003.11 - 9985136 Jul 19, 2018 (151)
41 ClinVar RCV000003596.4 Jul 19, 2018 (151)
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
ss1587721909 NC_000003.10:9960135:C= NC_000003.12:9943451:C= (self)
13904494, 7707104, 6777393, 130044179, 2547301, 7707104, ss342113199, ss488747055, ss491335442, ss780813362, ss783495410, ss978261287, ss1302761109, ss1584025775, ss1606392163, ss1649386196, ss1686863563, ss1711006722, ss1752488956, ss1917763169, ss1946074244, ss1958536051, ss2416033479, ss2733532566, ss2746943291, ss2789416425, ss2985246651, ss2991812945, ss3022210371, ss3628587466, ss3634879628, ss3640586931, ss3644806794 NC_000003.11:9985135:C= NC_000003.12:9943451:C= (self)
244446771, ss275513751, ss275516287, ss2248995598, ss3382405834, ss3382405835 NC_000003.12:9943451:C= NC_000003.12:9943451:C= (self)
244446771, ss2248995598, ss3382405834 NC_000003.12:9943451:C>G NC_000003.12:9943451:C>G (self)
ss1587721909 NC_000003.10:9960135:C>T NC_000003.12:9943451:C>T (self)
13904494, 7707104, 6777393, 130044179, 2547301, 7707104, ss342113199, ss488747055, ss491335442, ss780813362, ss783495410, ss978261287, ss1302761109, ss1584025775, ss1606392163, ss1649386196, ss1686863563, ss1711006722, ss1752488956, ss1917763169, ss1946074244, ss1958536051, ss2416033479, ss2733532566, ss2746943291, ss2789416425, ss2985246651, ss2991812945, ss3022210371, ss3628587466, ss3634879628, ss3640586931, ss3644806794 NC_000003.11:9985135:C>T NC_000003.12:9943451:C>T (self)
RCV000003596.4, 244446771, ss275513751, ss275516287, ss2248995598, ss3382405835 NC_000003.12:9943451:C>T NC_000003.12:9943451: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.

5 citations for rs28942091
PMID Title Author Year Journal
11376440 Genetic aspects of atrioventricular septal defects. Pierpont ME et al. 2000 American journal of medical genetics
12632326 Missense mutations in CRELD1 are associated with cardiac atrioventricular septal defects. Robinson SW et al. 2003 American journal of human genetics
17036335 CRELD1 mutations contribute to the occurrence of cardiac atrioventricular septal defects in Down syndrome. Maslen CL et al. 2006 American journal of medical genetics. Part A
23040494 An excess of deleterious variants in VEGF-A pathway genes in Down-syndrome-associated atrioventricular septal defects. Ackerman C et al. 2012 American journal of human genetics
24697899 Murine Creld1 controls cardiac development through activation of calcineurin/NFATc1 signaling. Mass E et al. 2014 Developmental cell

Genomic regions, transcripts, and products
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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: 0.1.4.post833+d3ba21e