6-32791520-G-A

Position:

• chr6-32791520-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 0.653 in 151,878 control chromosomes in the GnomAD database, including 32,524 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 0.65 (32524 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.81

Genes affected

(HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.716 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.32791520G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.653 AC: 99167 AN: 151760 Hom.: 32504 Cov.: 30

Gnomad AFR AF: 0.663

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.724

Gnomad FIN AF: 0.703

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.653 AC: 99228 AN: 151878 Hom.: 32524 Cov.: 30 AF XY: 0.658 AC XY: 48799 AN XY: 74212

Gnomad4 AFR AF: 0.662

Gnomad4 AMR AF: 0.631

Gnomad4 ASJ AF: 0.645

Gnomad4 EAS AF: 0.736

Gnomad4 SAS AF: 0.723

Gnomad4 FIN AF: 0.703

Gnomad4 NFE AF: 0.633

Gnomad4 OTH AF: 0.650

Alfa AF: 0.641 Hom.: 17377

Bravo AF: 0.647

Asia WGS AF: 0.739 AC: 2569 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	0.15
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2857161; hg19: chr6-32759297;