chr8-42680766-G-T

Position:

• chr8-42680766-G-T

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 0.666 in 151,998 control chromosomes in the GnomAD database, including 35,912 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 0.67 (35912 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.656

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.787 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.666 AC: 101152 AN: 151880 Hom.: 35893 Cov.: 31

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.817

Gnomad AMR AF: 0.727

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.806

Gnomad SAS AF: 0.723

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.779

Gnomad OTH AF: 0.689

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

GnomAD4 genome AF: 0.666 AC: 101204 AN: 151998 Hom.: 35912 Cov.: 31 AF XY: 0.670 AC XY: 49760 AN XY: 74298

Gnomad4 AFR AF: 0.401

Gnomad4 AMR AF: 0.727

Gnomad4 ASJ AF: 0.717

Gnomad4 EAS AF: 0.807

Gnomad4 SAS AF: 0.724

Gnomad4 FIN AF: 0.759

Gnomad4 NFE AF: 0.779

Gnomad4 OTH AF: 0.690

Alfa AF: 0.717 Hom.: 7618

Bravo AF: 0.651

Asia WGS AF: 0.721 AC: 2504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10958726; hg19: chr8-42535909;