13-72385256-C-T

Variant names:

• chr13-72385256-C-T
• rs4885001

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 0.697 in 151,864 control chromosomes in the GnomAD database, including 37,038 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 0.70 (37038 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.201
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.807 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: 0.697 AC: 105795 AN: 151744 Hom.: 37025 Cov.: 31

Gnomad AFR AF: 0.656

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.830

Gnomad FIN AF: 0.757

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.718

Gnomad OTH AF: 0.694

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

GnomAD4 genome AF: 0.697 AC: 105857 AN: 151864 Hom.: 37038 Cov.: 31 AF XY: 0.700 AC XY: 51945 AN XY: 74212

African (AFR) AF: 0.656 AC: 27156 AN: 41420

American (AMR) AF: 0.668 AC: 10162 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.646 AC: 2240 AN: 3468

East Asian (EAS) AF: 0.622 AC: 3197 AN: 5136

South Asian (SAS) AF: 0.829 AC: 3991 AN: 4816

European-Finnish (FIN) AF: 0.757 AC: 8011 AN: 10576

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.718 AC: 48762 AN: 67920

Other (OTH) AF: 0.698 AC: 1470 AN: 2106

Alfa AF: 0.709 Hom.: 165354

Bravo AF: 0.687

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.62
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs4885001; hg19: chr13-72959394; COSMIC: COSV64823389;