6-32713791-T-C

Variant names:

• chr6-32713791-T-C
• rs2647089

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 0.298 in 152,150 control chromosomes in the GnomAD database, including 7,209 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 0.30 (7209 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 22 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.44 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: 0.298 AC: 45281 AN: 152032 Hom.: 7211 Cov.: 32

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.298 AC: 45294 AN: 152150 Hom.: 7209 Cov.: 32 AF XY: 0.294 AC XY: 21852 AN XY: 74374

African (AFR) AF: 0.323 AC: 13386 AN: 41484

American (AMR) AF: 0.322 AC: 4926 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1370 AN: 3472

East Asian (EAS) AF: 0.406 AC: 2104 AN: 5182

South Asian (SAS) AF: 0.456 AC: 2194 AN: 4816

European-Finnish (FIN) AF: 0.121 AC: 1281 AN: 10596

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18794 AN: 67994

Other (OTH) AF: 0.365 AC: 772 AN: 2116

Alfa AF: 0.283 Hom.: 23688

Bravo AF: 0.312

Asia WGS AF: 0.456 AC: 1581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.0
DANN	Benign	0.45
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2647089; hg19: chr6-32681568;