rs3131513

Variant names:

• chr1-24866664-G-A
• rs3131513

Your query was ambiguous. Multiple possible variants found:

• chr1-24866664-G-A
• chr1-24866664-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.666 in 151,988 control chromosomes in the GnomAD database, including 34,550 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.67 (34550 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.819
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.81 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.665 AC: 101034 AN: 151870 Hom.: 34493 Cov.: 31

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.674

Gnomad EAS AF: 0.700

Gnomad SAS AF: 0.742

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.661

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.666 AC: 101150 AN: 151988 Hom.: 34550 Cov.: 31 AF XY: 0.664 AC XY: 49294 AN XY: 74268

African (AFR) AF: 0.817 AC: 33886 AN: 41468

American (AMR) AF: 0.569 AC: 8692 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.674 AC: 2339 AN: 3468

East Asian (EAS) AF: 0.700 AC: 3610 AN: 5156

South Asian (SAS) AF: 0.741 AC: 3565 AN: 4810

European-Finnish (FIN) AF: 0.559 AC: 5894 AN: 10540

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.604 AC: 41040 AN: 67956

Other (OTH) AF: 0.660 AC: 1395 AN: 2114

Alfa AF: 0.629 Hom.: 137617

Bravo AF: 0.670

Asia WGS AF: 0.717 AC: 2490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.53
PhyloP100		0.82

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3131513; hg19: chr1-25193155;