rs17439560

Variant names:

• chr15-37157418-G-A
• rs17439560

Your query was ambiguous. Multiple possible variants found:

• chr15-37157418-G-A
• chr15-37157418-G-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 0.101 in 131,066 control chromosomes in the GnomAD database, including 607 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 0.10 (607 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.328
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.107 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: 0.101 AC: 13265 AN: 130948 Hom.: 607 Cov.: 33

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.0160

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0719

Gnomad EAS AF: 0.0204

Gnomad SAS AF: 0.0711

Gnomad FIN AF: 0.0797

Gnomad MID AF: 0.0780

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.101 AC: 13274 AN: 131066 Hom.: 607 Cov.: 33 AF XY: 0.100 AC XY: 6378 AN XY: 63528

African (AFR) AF: 0.109 AC: 4162 AN: 38240

American (AMR) AF: 0.106 AC: 1375 AN: 13026

Ashkenazi Jewish (ASJ) AF: 0.0719 AC: 208 AN: 2894

East Asian (EAS) AF: 0.0204 AC: 90 AN: 4402

South Asian (SAS) AF: 0.0717 AC: 264 AN: 3684

European-Finnish (FIN) AF: 0.0797 AC: 677 AN: 8494

Middle Eastern (MID) AF: 0.0814 AC: 21 AN: 258

European-Non Finnish (NFE) AF: 0.109 AC: 6275 AN: 57486

Other (OTH) AF: 0.107 AC: 189 AN: 1768

Alfa AF: 0.0377 Hom.: 33

Bravo AF: 0.0920

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.90
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs17439560; hg19: chr15-37449619;