15-37157418-G-T

Variant names:

• chr15-37157418-G-T
• rs17439560

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The variant allele was found at a frequency of 0.00166 in 131,090 control chromosomes in the GnomAD database, including 3 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 0.0017 (3 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 -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BS2: High Homozygotes in GnomAd4 at 3 gene

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.00153 AC: 201 AN: 130972 Hom.: 1 Cov.: 33

Gnomad AFR AF: 0.00493

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000692

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000271

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000174

Gnomad OTH AF: 0.00114

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

GnomAD4 genome AF: 0.00166 AC: 218 AN: 131090 Hom.: 3 Cov.: 33 AF XY: 0.00164 AC XY: 104 AN XY: 63544

African (AFR) AF: 0.00536 AC: 205 AN: 38250

American (AMR) AF: 0.000691 AC: 9 AN: 13028

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2894

East Asian (EAS) AF: 0.00 AC: 0 AN: 4402

South Asian (SAS) AF: 0.000271 AC: 1 AN: 3684

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8498

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 258

European-Non Finnish (NFE) AF: 0.0000174 AC: 1 AN: 57494

Other (OTH) AF: 0.00113 AC: 2 AN: 1768

Alfa AF: 0.00 Hom.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.50
DANN	Benign	0.26
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;