6-32611193-T-C

Variant names:

• chr6-32611193-T-C
• rs502771

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 0.311 in 150,832 control chromosomes in the GnomAD database, including 7,685 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 0.31 (7685 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.277
• Publications: 41 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.311 AC: 46940 AN: 150716 Hom.: 7676 Cov.: 25

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.311 AC: 46982 AN: 150832 Hom.: 7685 Cov.: 25 AF XY: 0.309 AC XY: 22742 AN XY: 73670

African (AFR) AF: 0.379 AC: 15501 AN: 40924

American (AMR) AF: 0.277 AC: 4209 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1101 AN: 3466

East Asian (EAS) AF: 0.378 AC: 1914 AN: 5064

South Asian (SAS) AF: 0.336 AC: 1600 AN: 4764

European-Finnish (FIN) AF: 0.222 AC: 2312 AN: 10428

Middle Eastern (MID) AF: 0.472 AC: 137 AN: 290

European-Non Finnish (NFE) AF: 0.286 AC: 19340 AN: 67726

Other (OTH) AF: 0.330 AC: 688 AN: 2086

Alfa AF: 0.322 Hom.: 8239

Asia WGS AF: 0.319 AC: 1112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.9
DANN	Benign	0.48
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs502771; hg19: chr6-32578970;