chr13-73400826-G-A

Variant names:

• chr13-73400826-G-A
• rs965746

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 0.942 in 152,202 control chromosomes in the GnomAD database, including 67,652 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 0.94 (67652 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.782

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.96 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: 0.942 AC: 143193 AN: 152084 Hom.: 67589 Cov.: 31

Gnomad AFR AF: 0.916

Gnomad AMI AF: 0.928

Gnomad AMR AF: 0.965

Gnomad ASJ AF: 0.950

Gnomad EAS AF: 0.701

Gnomad SAS AF: 0.929

Gnomad FIN AF: 0.968

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.966

Gnomad OTH AF: 0.946

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

GnomAD4 genome AF: 0.942 AC: 143314 AN: 152202 Hom.: 67652 Cov.: 31 AF XY: 0.940 AC XY: 69960 AN XY: 74420

Gnomad4 AFR AF: 0.917

Gnomad4 AMR AF: 0.965

Gnomad4 ASJ AF: 0.950

Gnomad4 EAS AF: 0.701

Gnomad4 SAS AF: 0.929

Gnomad4 FIN AF: 0.968

Gnomad4 NFE AF: 0.966

Gnomad4 OTH AF: 0.947

Alfa AF: 0.958 Hom.: 8676

Bravo AF: 0.938

Asia WGS AF: 0.842 AC: 2928 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.1
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs965746; hg19: chr13-73974963;