6-32624423-T-C

Variant names:

• chr6-32624423-T-C
• rs9271640

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 0.762 in 151,652 control chromosomes in the GnomAD database, including 44,449 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 0.76 (44449 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 56 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 (NFE) allele frequency at 95% confidence interval = 0.803 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: 0.762 AC: 115509 AN: 151536 Hom.: 44422 Cov.: 30

Gnomad AFR AF: 0.667

Gnomad AMI AF: 0.897

Gnomad AMR AF: 0.808

Gnomad ASJ AF: 0.908

Gnomad EAS AF: 0.710

Gnomad SAS AF: 0.715

Gnomad FIN AF: 0.745

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.809

Gnomad OTH AF: 0.807

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

GnomAD4 genome AF: 0.762 AC: 115594 AN: 151652 Hom.: 44449 Cov.: 30 AF XY: 0.758 AC XY: 56160 AN XY: 74086

African (AFR) AF: 0.668 AC: 27572 AN: 41300

American (AMR) AF: 0.808 AC: 12315 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.908 AC: 3137 AN: 3456

East Asian (EAS) AF: 0.711 AC: 3662 AN: 5152

South Asian (SAS) AF: 0.716 AC: 3451 AN: 4818

European-Finnish (FIN) AF: 0.745 AC: 7825 AN: 10502

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.809 AC: 54877 AN: 67868

Other (OTH) AF: 0.803 AC: 1694 AN: 2110

Alfa AF: 0.792 Hom.: 92688

Bravo AF: 0.765

Asia WGS AF: 0.649 AC: 2262 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	8.9
DANN	Benign	0.61
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs9271640; hg19: chr6-32592200; COSMIC: COSV70073303;