chr8-6938679-C-T

Variant names:

• chr8-6938679-C-T
• rs2741676

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 0.21 in 151,998 control chromosomes in the GnomAD database, including 3,631 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 0.21 (3631 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0940

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.293 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: 0.210 AC: 31948 AN: 151878 Hom.: 3638 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.210 AC: 31939 AN: 151998 Hom.: 3631 Cov.: 32 AF XY: 0.211 AC XY: 15645 AN XY: 74272

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.281

Gnomad4 EAS AF: 0.306

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.242

Gnomad4 NFE AF: 0.243

Gnomad4 OTH AF: 0.212

Alfa AF: 0.231 Hom.: 822

Bravo AF: 0.202

Asia WGS AF: 0.272 AC: 947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.4
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2741676; hg19: chr8-6796201;