chr6-32605694-A-G

Position:

• chr6-32605694-A-G

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 0.689 in 151,700 control chromosomes in the GnomAD database, including 36,304 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 0.69 (36304 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.748 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: 0.689 AC: 104514 AN: 151582 Hom.: 36275 Cov.: 28

Gnomad AFR AF: 0.755

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.715

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

GnomAD4 genome AF: 0.689 AC: 104590 AN: 151700 Hom.: 36304 Cov.: 28 AF XY: 0.684 AC XY: 50727 AN XY: 74114

Gnomad4 AFR AF: 0.755

Gnomad4 AMR AF: 0.628

Gnomad4 ASJ AF: 0.617

Gnomad4 EAS AF: 0.741

Gnomad4 SAS AF: 0.672

Gnomad4 FIN AF: 0.606

Gnomad4 NFE AF: 0.677

Gnomad4 OTH AF: 0.711

Alfa AF: 0.680 Hom.: 5353

Bravo AF: 0.696

Asia WGS AF: 0.665 AC: 2315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.19
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9270965; hg19: chr6-32573471;