6-32411163-C-T

Position:

• chr6-32411163-C-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 0.718 in 152,000 control chromosomes in the GnomAD database, including 39,345 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 0.72 (39345 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.180

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.32411163C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.718 AC: 109042 AN: 151884 Hom.: 39325 Cov.: 31

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.691

Gnomad ASJ AF: 0.696

Gnomad EAS AF: 0.731

Gnomad SAS AF: 0.710

Gnomad FIN AF: 0.755

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.687

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.718 AC: 109106 AN: 152000 Hom.: 39345 Cov.: 31 AF XY: 0.717 AC XY: 53296 AN XY: 74288

Gnomad4 AFR AF: 0.770

Gnomad4 AMR AF: 0.691

Gnomad4 ASJ AF: 0.696

Gnomad4 EAS AF: 0.732

Gnomad4 SAS AF: 0.710

Gnomad4 FIN AF: 0.755

Gnomad4 NFE AF: 0.687

Gnomad4 OTH AF: 0.715

Alfa AF: 0.687 Hom.: 40618

Bravo AF: 0.721

Asia WGS AF: 0.717 AC: 2496 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.4
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3129961; hg19: chr6-32378940;