6-62531379-C-T

Variant names:

• chr6-62531379-C-T
• rs6902361

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 0.507 in 151,744 control chromosomes in the GnomAD database, including 20,020 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 0.51 (20020 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.213
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.592 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: 0.507 AC: 76901 AN: 151626 Hom.: 20004 Cov.: 31

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.507 AC: 76954 AN: 151744 Hom.: 20020 Cov.: 31 AF XY: 0.508 AC XY: 37661 AN XY: 74118

African (AFR) AF: 0.599 AC: 24758 AN: 41350

American (AMR) AF: 0.361 AC: 5507 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.490 AC: 1698 AN: 3466

East Asian (EAS) AF: 0.338 AC: 1734 AN: 5130

South Asian (SAS) AF: 0.449 AC: 2161 AN: 4812

European-Finnish (FIN) AF: 0.623 AC: 6551 AN: 10514

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.483 AC: 32819 AN: 67914

Other (OTH) AF: 0.481 AC: 1014 AN: 2108

Alfa AF: 0.510 Hom.: 2580

Bravo AF: 0.492

Asia WGS AF: 0.370 AC: 1291 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	5.0
DANN	Benign	0.73
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs6902361; hg19: chr6-63241284;