chr6-32988943-T-C

Variant names:

• chr6-32988943-T-C
• rs497058

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 0.635 in 151,826 control chromosomes in the GnomAD database, including 31,887 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 0.64 (31887 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.531
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.823 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: 0.635 AC: 96331 AN: 151708 Hom.: 31836 Cov.: 30

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.635 AC: 96432 AN: 151826 Hom.: 31887 Cov.: 30 AF XY: 0.631 AC XY: 46819 AN XY: 74226

African (AFR) AF: 0.830 AC: 34304 AN: 41322

American (AMR) AF: 0.540 AC: 8245 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.607 AC: 2104 AN: 3466

East Asian (EAS) AF: 0.479 AC: 2479 AN: 5176

South Asian (SAS) AF: 0.481 AC: 2315 AN: 4810

European-Finnish (FIN) AF: 0.613 AC: 6448 AN: 10516

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.567 AC: 38555 AN: 67966

Other (OTH) AF: 0.633 AC: 1330 AN: 2102

Alfa AF: 0.620 Hom.: 3759

Bravo AF: 0.639

Asia WGS AF: 0.514 AC: 1788 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.4
DANN	Benign	0.77
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs497058; hg19: chr6-32956720; COSMIC: COSV53487862;