15-87083881-T-G

Variant names:

• chr15-87083881-T-G
• rs1034482

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 0.0962 in 151,946 control chromosomes in the GnomAD database, including 810 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 0.096 (810 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.528
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.155 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: 0.0961 AC: 14592 AN: 151826 Hom.: 805 Cov.: 32

Gnomad AFR AF: 0.0941

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.0831

Gnomad SAS AF: 0.0359

Gnomad FIN AF: 0.0850

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0867

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.0962 AC: 14612 AN: 151946 Hom.: 810 Cov.: 32 AF XY: 0.0956 AC XY: 7097 AN XY: 74236

African (AFR) AF: 0.0940 AC: 3899 AN: 41460

American (AMR) AF: 0.160 AC: 2437 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 516 AN: 3466

East Asian (EAS) AF: 0.0832 AC: 429 AN: 5154

South Asian (SAS) AF: 0.0370 AC: 178 AN: 4812

European-Finnish (FIN) AF: 0.0850 AC: 897 AN: 10556

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0867 AC: 5891 AN: 67936

Other (OTH) AF: 0.101 AC: 213 AN: 2114

Alfa AF: 0.0880 Hom.: 386

Bravo AF: 0.102

Asia WGS AF: 0.0560 AC: 198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.3
DANN	Benign	0.38
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs1034482; hg19: chr15-87627112;