rs759258

Variant names:

• chr17-57051187-A-C
• rs759258

Your query was ambiguous. Multiple possible variants found:

• chr17-57051187-A-C
• chr17-57051187-A-G
• chr17-57051187-A-T

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 0.737 in 151,718 control chromosomes in the GnomAD database, including 41,637 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 0.74 (41637 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.662
• Publications: 10 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 (EAS) allele frequency at 95% confidence interval = 0.849 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: 0.737 AC: 111779 AN: 151606 Hom.: 41607 Cov.: 30

Gnomad AFR AF: 0.626

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.807

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.869

Gnomad SAS AF: 0.824

Gnomad FIN AF: 0.743

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.772

Gnomad OTH AF: 0.756

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

GnomAD4 genome AF: 0.737 AC: 111854 AN: 151718 Hom.: 41637 Cov.: 30 AF XY: 0.739 AC XY: 54772 AN XY: 74112

African (AFR) AF: 0.626 AC: 25856 AN: 41296

American (AMR) AF: 0.807 AC: 12272 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.710 AC: 2466 AN: 3472

East Asian (EAS) AF: 0.870 AC: 4507 AN: 5180

South Asian (SAS) AF: 0.824 AC: 3964 AN: 4810

European-Finnish (FIN) AF: 0.743 AC: 7778 AN: 10474

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.772 AC: 52470 AN: 67972

Other (OTH) AF: 0.756 AC: 1590 AN: 2102

Alfa AF: 0.765 Hom.: 29956

Bravo AF: 0.735

Asia WGS AF: 0.816 AC: 2835 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	1.6
DANN	Benign	0.47
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs759258; hg19: chr17-55128548;