6-159294171-C-T

Position:

• chr6-159294171-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 0.719 in 152,052 control chromosomes in the GnomAD database, including 41,298 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 (41298 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.817 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: 0.720 AC: 109360 AN: 151934 Hom.: 41289 Cov.: 32

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.723

Gnomad AMR AF: 0.806

Gnomad ASJ AF: 0.830

Gnomad EAS AF: 0.670

Gnomad SAS AF: 0.795

Gnomad FIN AF: 0.852

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.823

Gnomad OTH AF: 0.752

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

GnomAD4 genome AF: 0.719 AC: 109396 AN: 152052 Hom.: 41298 Cov.: 32 AF XY: 0.725 AC XY: 53867 AN XY: 74344

Gnomad4 AFR AF: 0.470

Gnomad4 AMR AF: 0.806

Gnomad4 ASJ AF: 0.830

Gnomad4 EAS AF: 0.669

Gnomad4 SAS AF: 0.794

Gnomad4 FIN AF: 0.852

Gnomad4 NFE AF: 0.823

Gnomad4 OTH AF: 0.755

Alfa AF: 0.775 Hom.: 5827

Bravo AF: 0.707

Asia WGS AF: 0.726 AC: 2528 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.79
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: rs579533; hg19: chr6-159715203; COSMIC: COSV60298311;