rs2752976

Variant names:

• chr6-62718524-T-C
• rs2752976

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 0.546 in 152,030 control chromosomes in the GnomAD database, including 23,390 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 0.55 (23390 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0750
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.546 AC: 82976 AN: 151914 Hom.: 23365 Cov.: 32

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.735

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.515

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.546 AC: 83045 AN: 152030 Hom.: 23390 Cov.: 32 AF XY: 0.542 AC XY: 40280 AN XY: 74282

African (AFR) AF: 0.686 AC: 28429 AN: 41448

American (AMR) AF: 0.394 AC: 6024 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.515 AC: 1787 AN: 3468

East Asian (EAS) AF: 0.343 AC: 1770 AN: 5166

South Asian (SAS) AF: 0.459 AC: 2212 AN: 4822

European-Finnish (FIN) AF: 0.586 AC: 6187 AN: 10562

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.511 AC: 34715 AN: 67976

Other (OTH) AF: 0.518 AC: 1092 AN: 2110

Alfa AF: 0.524 Hom.: 3674

Bravo AF: 0.540

Asia WGS AF: 0.399 AC: 1388 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.5
DANN	Benign	0.74
PhyloP100		0.075

Splicing

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

Other links and lift over

dbSNP: rs2752976; hg19: chr6-63428429;