13-73272131-T-G

Variant names:

• chr13-73272131-T-G
• rs1330082

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 0.637 in 151,836 control chromosomes in the GnomAD database, including 31,198 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 0.64 (31198 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.806 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: 0.637 AC: 96674 AN: 151718 Hom.: 31175 Cov.: 31

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.679

Gnomad EAS AF: 0.827

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.666

Gnomad NFE AF: 0.627

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.637 AC: 96753 AN: 151836 Hom.: 31198 Cov.: 31 AF XY: 0.641 AC XY: 47547 AN XY: 74186

African (AFR) AF: 0.581 AC: 24058 AN: 41396

American (AMR) AF: 0.748 AC: 11394 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.679 AC: 2357 AN: 3472

East Asian (EAS) AF: 0.827 AC: 4259 AN: 5152

South Asian (SAS) AF: 0.769 AC: 3705 AN: 4818

European-Finnish (FIN) AF: 0.592 AC: 6252 AN: 10552

Middle Eastern (MID) AF: 0.661 AC: 193 AN: 292

European-Non Finnish (NFE) AF: 0.627 AC: 42616 AN: 67916

Other (OTH) AF: 0.683 AC: 1437 AN: 2104

Alfa AF: 0.630 Hom.: 12962

Bravo AF: 0.650

Asia WGS AF: 0.778 AC: 2706 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.41
DANN	Benign	0.36
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1330082; hg19: chr13-73846268;