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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.817

Gnomad4 AMR AF: 0.569

Gnomad4 ASJ AF: 0.674

Gnomad4 EAS AF: 0.700

Gnomad4 SAS AF: 0.741

Gnomad4 FIN AF: 0.559

Gnomad4 NFE AF: 0.604

Gnomad4 OTH AF: 0.660

Alfa AF: 0.621 Hom.: 62745

Bravo AF: 0.670

Asia WGS AF: 0.717 AC: 2490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3131513; hg19: chr1-25193155;