chr15-57951485-G-A

Variant names:

• chr15-57951485-G-A
• rs7169289

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 0.823 in 152,056 control chromosomes in the GnomAD database, including 51,460 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 0.82 (51460 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.54
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• 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: 0.823 AC: 125021 AN: 151938 Hom.: 51399 Cov.: 30

Gnomad AFR AF: 0.844

Gnomad AMI AF: 0.805

Gnomad AMR AF: 0.820

Gnomad ASJ AF: 0.789

Gnomad EAS AF: 0.750

Gnomad SAS AF: 0.741

Gnomad FIN AF: 0.845

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.821

Gnomad OTH AF: 0.820

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

GnomAD4 genome AF: 0.823 AC: 125146 AN: 152056 Hom.: 51460 Cov.: 30 AF XY: 0.821 AC XY: 61021 AN XY: 74302

African (AFR) AF: 0.844 AC: 35020 AN: 41484

American (AMR) AF: 0.820 AC: 12530 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.789 AC: 2734 AN: 3466

East Asian (EAS) AF: 0.749 AC: 3866 AN: 5162

South Asian (SAS) AF: 0.742 AC: 3570 AN: 4812

European-Finnish (FIN) AF: 0.845 AC: 8928 AN: 10570

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.821 AC: 55798 AN: 67974

Other (OTH) AF: 0.822 AC: 1735 AN: 2110

Alfa AF: 0.818 Hom.: 59697

Bravo AF: 0.822

Asia WGS AF: 0.769 AC: 2677 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.13
DANN	Benign	0.51
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs7169289; hg19: chr15-58243683;