15-53349495-C-T

Variant names:

• chr15-53349495-C-T
• rs272764

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 0.461 in 152,010 control chromosomes in the GnomAD database, including 16,179 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 0.46 (16179 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.594
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.557 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: 0.461 AC: 69989 AN: 151892 Hom.: 16175 Cov.: 33

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.574

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.461 AC: 70018 AN: 152010 Hom.: 16179 Cov.: 33 AF XY: 0.462 AC XY: 34317 AN XY: 74294

African (AFR) AF: 0.429 AC: 17806 AN: 41466

American (AMR) AF: 0.495 AC: 7574 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.447 AC: 1549 AN: 3468

East Asian (EAS) AF: 0.574 AC: 2967 AN: 5170

South Asian (SAS) AF: 0.493 AC: 2373 AN: 4818

European-Finnish (FIN) AF: 0.447 AC: 4709 AN: 10528

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.465 AC: 31621 AN: 67954

Other (OTH) AF: 0.470 AC: 989 AN: 2106

Alfa AF: 0.301 Hom.: 747

Bravo AF: 0.461

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	9.6
DANN	Benign	0.81
PhyloP100		0.59

Splicing

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

Other links and lift over

dbSNP: rs272764; hg19: chr15-53641692;