6-32241250-T-C

Variant names:

• chr6-32241250-T-C
• rs382259

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 0.32 in 151,934 control chromosomes in the GnomAD database, including 8,649 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 0.32 (8649 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.224
• Publications: 36 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.507 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: 0.320 AC: 48531 AN: 151816 Hom.: 8645 Cov.: 31

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.320 AC: 48568 AN: 151934 Hom.: 8649 Cov.: 31 AF XY: 0.321 AC XY: 23835 AN XY: 74294

African (AFR) AF: 0.355 AC: 14698 AN: 41406

American (AMR) AF: 0.378 AC: 5771 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.661 AC: 2292 AN: 3466

East Asian (EAS) AF: 0.433 AC: 2239 AN: 5170

South Asian (SAS) AF: 0.525 AC: 2520 AN: 4804

European-Finnish (FIN) AF: 0.157 AC: 1659 AN: 10576

Middle Eastern (MID) AF: 0.579 AC: 169 AN: 292

European-Non Finnish (NFE) AF: 0.267 AC: 18152 AN: 67946

Other (OTH) AF: 0.399 AC: 844 AN: 2114

Alfa AF: 0.303 Hom.: 12845

Bravo AF: 0.336

Asia WGS AF: 0.446 AC: 1553 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.7
DANN	Benign	0.69
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs382259; hg19: chr6-32209027;