chr8-6938679-C-T

Variant names:

• chr8-6938679-C-T
• rs2741676

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 0.21 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
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.293 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: 0.210 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

African (AFR) AF: 0.135 AC: 5586 AN: 41506

American (AMR) AF: 0.179 AC: 2742 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 975 AN: 3470

East Asian (EAS) AF: 0.306 AC: 1577 AN: 5156

South Asian (SAS) AF: 0.237 AC: 1136 AN: 4790

European-Finnish (FIN) AF: 0.242 AC: 2549 AN: 10544

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16483 AN: 67942

Other (OTH) AF: 0.212 AC: 447 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.4
DANN	Benign	0.36
PhyloP100		-0.094
PromoterAI		0.0022	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2741676; hg19: chr8-6796201;