6-32572264-T-C

Variant names:

• chr6-32572264-T-C
• rs9269329

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.699

Gnomad4 AMR AF: 0.642

Gnomad4 ASJ AF: 0.647

Gnomad4 EAS AF: 0.597

Gnomad4 SAS AF: 0.621

Gnomad4 FIN AF: 0.582

Gnomad4 NFE AF: 0.609

Gnomad4 OTH AF: 0.640

Alfa AF: 0.644 Hom.: 2712

Asia WGS AF: 0.530 AC: 1297 AN: 2442

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9269329; hg19: chr6-32540041;