chr6-32670538-G-A

Position:

• chr6-32670538-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 0.471 in 148,490 control chromosomes in the GnomAD database, including 18,894 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 0.47 (18894 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.619

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.739 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: 0.472 AC: 69963 AN: 148374 Hom.: 18887 Cov.: 29

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.547

Gnomad EAS AF: 0.759

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.471 AC: 70006 AN: 148490 Hom.: 18894 Cov.: 29 AF XY: 0.475 AC XY: 34387 AN XY: 72416

Gnomad4 AFR AF: 0.461

Gnomad4 AMR AF: 0.580

Gnomad4 ASJ AF: 0.547

Gnomad4 EAS AF: 0.759

Gnomad4 SAS AF: 0.545

Gnomad4 FIN AF: 0.426

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.495

Alfa AF: 0.446 Hom.: 3862

Asia WGS AF: 0.638 AC: 2188 AN: 3434

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.5
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9274759; hg19: chr6-32638315;