6-159294171-C-T

Variant names:

• chr6-159294171-C-T
• rs579533

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;