chr6-32713500-A-G

Position:

• chr6-32713500-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 0.427 in 151,956 control chromosomes in the GnomAD database, including 14,205 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 0.43 (14205 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.140

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.518 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: 0.427 AC: 64766 AN: 151836 Hom.: 14197 Cov.: 31

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.427 AC: 64810 AN: 151956 Hom.: 14205 Cov.: 31 AF XY: 0.424 AC XY: 31543 AN XY: 74312

Gnomad4 AFR AF: 0.474

Gnomad4 AMR AF: 0.438

Gnomad4 ASJ AF: 0.527

Gnomad4 EAS AF: 0.435

Gnomad4 SAS AF: 0.535

Gnomad4 FIN AF: 0.328

Gnomad4 NFE AF: 0.392

Gnomad4 OTH AF: 0.500

Alfa AF: 0.406 Hom.: 17735

Bravo AF: 0.435

Asia WGS AF: 0.520 AC: 1810 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.0
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2858331; hg19: chr6-32681277;