6-153756058-C-T

Variant names:

• chr6-153756058-C-T
• rs1937579

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 0.761 in 152,154 control chromosomes in the GnomAD database, including 44,397 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 0.76 (44397 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.330
• Publications: 6 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 (AFR) allele frequency at 95% confidence interval = 0.837 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: 0.761 AC: 115698 AN: 152036 Hom.: 44363 Cov.: 33

Gnomad AFR AF: 0.845

Gnomad AMI AF: 0.633

Gnomad AMR AF: 0.826

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.782

Gnomad SAS AF: 0.787

Gnomad FIN AF: 0.752

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.779

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

GnomAD4 genome AF: 0.761 AC: 115789 AN: 152154 Hom.: 44397 Cov.: 33 AF XY: 0.765 AC XY: 56896 AN XY: 74398

African (AFR) AF: 0.845 AC: 35092 AN: 41546

American (AMR) AF: 0.826 AC: 12608 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.724 AC: 2512 AN: 3468

East Asian (EAS) AF: 0.782 AC: 4042 AN: 5170

South Asian (SAS) AF: 0.788 AC: 3799 AN: 4824

European-Finnish (FIN) AF: 0.752 AC: 7954 AN: 10580

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.696 AC: 47330 AN: 67978

Other (OTH) AF: 0.776 AC: 1640 AN: 2114

Alfa AF: 0.734 Hom.: 12151

Bravo AF: 0.770

Asia WGS AF: 0.803 AC: 2791 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	0.86
DANN	Benign	0.33
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs1937579; hg19: chr6-154077193;