6-32693166-A-G

Position:

• chr6-32693166-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 0.536 in 151,738 control chromosomes in the GnomAD database, including 22,231 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 0.54 (22231 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.629

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.635 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: 0.536 AC: 81241 AN: 151620 Hom.: 22210 Cov.: 30

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.713

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.536 AC: 81318 AN: 151738 Hom.: 22231 Cov.: 30 AF XY: 0.540 AC XY: 40075 AN XY: 74158

Gnomad4 AFR AF: 0.524

Gnomad4 AMR AF: 0.634

Gnomad4 ASJ AF: 0.615

Gnomad4 EAS AF: 0.653

Gnomad4 SAS AF: 0.416

Gnomad4 FIN AF: 0.615

Gnomad4 NFE AF: 0.502

Gnomad4 OTH AF: 0.554

Alfa AF: 0.515 Hom.: 16028

Bravo AF: 0.543

Asia WGS AF: 0.595 AC: 2070 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.5
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9275245; hg19: chr6-32660943; COSMIC: COSV70886663;