rs6931798

Variant names:

• chr6-40697676-C-T
• rs6931798

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 0.264 in 152,108 control chromosomes in the GnomAD database, including 5,997 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 0.26 (5997 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.951
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40110 AN: 151990 Hom.: 5984 Cov.: 33

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.264 AC: 40138 AN: 152108 Hom.: 5997 Cov.: 33 AF XY: 0.265 AC XY: 19700 AN XY: 74350

African (AFR) AF: 0.403 AC: 16689 AN: 41458

American (AMR) AF: 0.248 AC: 3792 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 693 AN: 3470

East Asian (EAS) AF: 0.295 AC: 1526 AN: 5174

South Asian (SAS) AF: 0.398 AC: 1919 AN: 4826

European-Finnish (FIN) AF: 0.156 AC: 1654 AN: 10590

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.192 AC: 13080 AN: 67998

Other (OTH) AF: 0.279 AC: 588 AN: 2106

Alfa AF: 0.218 Hom.: 14138

Bravo AF: 0.272

Asia WGS AF: 0.356 AC: 1242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	11
DANN	Benign	0.77
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs6931798; hg19: chr6-40665415;