chr13-70491962-A-G

Position:

• chr13-70491962-A-G

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 0.736 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.608

Gnomad4 AMR AF: 0.703

Gnomad4 ASJ AF: 0.837

Gnomad4 EAS AF: 0.619

Gnomad4 SAS AF: 0.814

Gnomad4 FIN AF: 0.796

Gnomad4 NFE AF: 0.811

Gnomad4 OTH AF: 0.754

Alfa AF: 0.751 Hom.: 6854

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

Splicing

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

Publications

LitVar

Other links and lift over

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