6-32606531-C-T

Position:

• chr6-32606531-C-T

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 0.627 in 151,898 control chromosomes in the GnomAD database, including 30,143 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 0.63 (30143 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.159

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.742 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.627 AC: 95209 AN: 151780 Hom.: 30105 Cov.: 31

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.460

Gnomad AMR AF: 0.686

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.761

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.748

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.627 AC: 95298 AN: 151898 Hom.: 30143 Cov.: 31 AF XY: 0.629 AC XY: 46648 AN XY: 74214

Gnomad4 AFR AF: 0.647

Gnomad4 AMR AF: 0.686

Gnomad4 ASJ AF: 0.663

Gnomad4 EAS AF: 0.761

Gnomad4 SAS AF: 0.560

Gnomad4 FIN AF: 0.607

Gnomad4 NFE AF: 0.599

Gnomad4 OTH AF: 0.641

Alfa AF: 0.611 Hom.: 7775

Bravo AF: 0.635

Asia WGS AF: 0.633 AC: 2204 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.40
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2760994; hg19: chr6-32574308;