6-32607592-G-T

Position:

• chr6-32607592-G-T

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 0.845 in 151,006 control chromosomes in the GnomAD database, including 53,923 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 0.84 (53923 hom., cov: 26)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.745

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.869 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.32607592G>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.845 AC: 127446 AN: 150892 Hom.: 53880 Cov.: 26

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.909

Gnomad AMR AF: 0.881

Gnomad ASJ AF: 0.917

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.858

Gnomad MID AF: 0.900

Gnomad NFE AF: 0.841

Gnomad OTH AF: 0.874

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

GnomAD4 genome AF: 0.845 AC: 127539 AN: 151006 Hom.: 53923 Cov.: 26 AF XY: 0.843 AC XY: 62142 AN XY: 73690

Gnomad4 AFR AF: 0.837

Gnomad4 AMR AF: 0.881

Gnomad4 ASJ AF: 0.917

Gnomad4 EAS AF: 0.820

Gnomad4 SAS AF: 0.765

Gnomad4 FIN AF: 0.858

Gnomad4 NFE AF: 0.841

Gnomad4 OTH AF: 0.869

Alfa AF: 0.846 Hom.: 45353

Bravo AF: 0.850

Asia WGS AF: 0.746 AC: 2597 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	10
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9271055; hg19: chr6-32575369;