rs914904

Variant names:

• chr13-70491962-A-G
• rs914904

Your query was ambiguous. Multiple possible variants found:

• chr13-70491962-A-G
• chr13-70491962-A-T

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 0.736 in 151,998 control chromosomes in the GnomAD database, including 41,951 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 0.74 (41951 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.805 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: 0.736 AC: 111832 AN: 151880 Hom.: 41942 Cov.: 31

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.660

Gnomad AMR AF: 0.703

Gnomad ASJ AF: 0.837

Gnomad EAS AF: 0.618

Gnomad SAS AF: 0.815

Gnomad FIN AF: 0.796

Gnomad MID AF: 0.847

Gnomad NFE AF: 0.811

Gnomad OTH AF: 0.753

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

GnomAD4 genome AF: 0.736 AC: 111893 AN: 151998 Hom.: 41951 Cov.: 31 AF XY: 0.737 AC XY: 54717 AN XY: 74288

African (AFR) AF: 0.608 AC: 25185 AN: 41444

American (AMR) AF: 0.703 AC: 10742 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.837 AC: 2899 AN: 3464

East Asian (EAS) AF: 0.619 AC: 3193 AN: 5162

South Asian (SAS) AF: 0.814 AC: 3918 AN: 4814

European-Finnish (FIN) AF: 0.796 AC: 8395 AN: 10550

Middle Eastern (MID) AF: 0.853 AC: 249 AN: 292

European-Non Finnish (NFE) AF: 0.811 AC: 55122 AN: 67980

Other (OTH) AF: 0.754 AC: 1591 AN: 2110

Alfa AF: 0.746 Hom.: 6993

Bravo AF: 0.720

Asia WGS AF: 0.732 AC: 2542 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
DANN	Benign	0.44
PhyloP100		-0.048

Splicing

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

Other links and lift over

dbSNP: rs914904; hg19: chr13-71066094; COSMIC: COSV69362358;