6-32572264-T-C

Position:

• chr6-32572264-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;