6-81354748-C-T

Variant names:

• chr6-81354748-C-T
• rs962983

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.680 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

Gnomad4 AFR AF: 0.502

Gnomad4 AMR AF: 0.721

Gnomad4 ASJ AF: 0.730

Gnomad4 EAS AF: 0.667

Gnomad4 SAS AF: 0.682

Gnomad4 FIN AF: 0.828

Gnomad4 NFE AF: 0.751

Gnomad4 OTH AF: 0.681

Alfa AF: 0.734 Hom.: 66917

Bravo AF: 0.664

Asia WGS AF: 0.664 AC: 2309 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs962983; hg19: chr6-82064465;