6-32572264-T-C

Variant names:

• chr6-32572264-T-C
• rs9269329

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 0.639 in 93,680 control chromosomes in the GnomAD database, including 17,252 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 (17252 hom., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 8 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 (AFR) allele frequency at 95% confidence interval = 0.691 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: 0.639 AC: 59840 AN: 93586 Hom.: 17229 Cov.: 21

Gnomad AFR AF: 0.699

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.647

Gnomad EAS AF: 0.597

Gnomad SAS AF: 0.619

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.746

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.639 AC: 59898 AN: 93680 Hom.: 17252 Cov.: 21 AF XY: 0.638 AC XY: 28988 AN XY: 45418

African (AFR) AF: 0.699 AC: 20200 AN: 28912

American (AMR) AF: 0.642 AC: 5382 AN: 8384

Ashkenazi Jewish (ASJ) AF: 0.647 AC: 1352 AN: 2090

East Asian (EAS) AF: 0.597 AC: 1721 AN: 2884

South Asian (SAS) AF: 0.621 AC: 1953 AN: 3146

European-Finnish (FIN) AF: 0.582 AC: 3210 AN: 5518

Middle Eastern (MID) AF: 0.741 AC: 163 AN: 220

European-Non Finnish (NFE) AF: 0.609 AC: 24820 AN: 40746

Other (OTH) AF: 0.640 AC: 845 AN: 1320

Alfa AF: 0.644 Hom.: 2712

Asia WGS AF: 0.530 AC: 1297 AN: 2442

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.55
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs9269329; hg19: chr6-32540041;