6-32615965-G-A

Position:

• chr6-32615965-G-A

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 0.739 in 151,916 control chromosomes in the GnomAD database, including 41,720 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 0.74 (41720 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.946

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.796 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: 0.739 AC: 112121 AN: 151798 Hom.: 41669 Cov.: 30

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.802

Gnomad ASJ AF: 0.803

Gnomad EAS AF: 0.817

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.816

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.746

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

GnomAD4 genome AF: 0.739 AC: 112231 AN: 151916 Hom.: 41720 Cov.: 30 AF XY: 0.742 AC XY: 55105 AN XY: 74256

Gnomad4 AFR AF: 0.734

Gnomad4 AMR AF: 0.802

Gnomad4 ASJ AF: 0.803

Gnomad4 EAS AF: 0.817

Gnomad4 SAS AF: 0.610

Gnomad4 FIN AF: 0.816

Gnomad4 NFE AF: 0.715

Gnomad4 OTH AF: 0.747

Alfa AF: 0.730 Hom.: 32753

Bravo AF: 0.739

Asia WGS AF: 0.710 AC: 2474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.3
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9271348; hg19: chr6-32583742;