rs965746

Variant names:

• chr13-73400826-G-A
• rs965746

Your query was ambiguous. Multiple possible variants found:

• chr13-73400826-G-A
• chr13-73400826-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 0.942 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.917 AC: 38046 AN: 41508

American (AMR) AF: 0.965 AC: 14772 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.950 AC: 3298 AN: 3470

East Asian (EAS) AF: 0.701 AC: 3605 AN: 5142

South Asian (SAS) AF: 0.929 AC: 4481 AN: 4824

European-Finnish (FIN) AF: 0.968 AC: 10262 AN: 10606

Middle Eastern (MID) AF: 0.939 AC: 276 AN: 294

European-Non Finnish (NFE) AF: 0.966 AC: 65727 AN: 68028

Other (OTH) AF: 0.947 AC: 2001 AN: 2114

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
PhyloP100		0.78

Splicing

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

Other links and lift over

dbSNP: rs965746; hg19: chr13-73974963;