6-159294171-C-T

Variant names:

• chr6-159294171-C-T
• rs579533

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.470 AC: 19478 AN: 41432

American (AMR) AF: 0.806 AC: 12318 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.830 AC: 2880 AN: 3470

East Asian (EAS) AF: 0.669 AC: 3466 AN: 5180

South Asian (SAS) AF: 0.794 AC: 3837 AN: 4830

European-Finnish (FIN) AF: 0.852 AC: 9009 AN: 10578

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.823 AC: 55928 AN: 67966

Other (OTH) AF: 0.755 AC: 1592 AN: 2110

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
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs579533; hg19: chr6-159715203; COSMIC: COSV60298311;