6-81354748-C-T

Variant names:

• chr6-81354748-C-T
• rs962983

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 0.679 in 151,916 control chromosomes in the GnomAD database, including 36,080 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 0.68 (36080 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.553
• Publications: 5 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 (NFE) allele frequency at 95% confidence interval = 0.746 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.680 AC: 103163 AN: 151798 Hom.: 36080 Cov.: 32

Gnomad AFR AF: 0.503

Gnomad AMI AF: 0.806

Gnomad AMR AF: 0.722

Gnomad ASJ AF: 0.730

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.828

Gnomad MID AF: 0.640

Gnomad NFE AF: 0.751

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.679 AC: 103190 AN: 151916 Hom.: 36080 Cov.: 32 AF XY: 0.682 AC XY: 50697 AN XY: 74284

African (AFR) AF: 0.502 AC: 20814 AN: 41436

American (AMR) AF: 0.721 AC: 10996 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.730 AC: 2528 AN: 3462

East Asian (EAS) AF: 0.667 AC: 3438 AN: 5156

South Asian (SAS) AF: 0.682 AC: 3288 AN: 4822

European-Finnish (FIN) AF: 0.828 AC: 8769 AN: 10596

Middle Eastern (MID) AF: 0.634 AC: 185 AN: 292

European-Non Finnish (NFE) AF: 0.751 AC: 51000 AN: 67882

Other (OTH) AF: 0.681 AC: 1437 AN: 2110

Alfa AF: 0.725 Hom.: 150947

Bravo AF: 0.664

Asia WGS AF: 0.664 AC: 2309 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.33
DANN	Benign	0.26
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs962983; hg19: chr6-82064465;