chr15-42059955-G-A

Variant names:

• chr15-42059955-G-A
• rs8042219

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 0.177 in 152,088 control chromosomes in the GnomAD database, including 2,434 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 0.18 (2434 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.744
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.185 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: 0.177 AC: 26897 AN: 151970 Hom.: 2437 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.0891

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.177 AC: 26901 AN: 152088 Hom.: 2434 Cov.: 32 AF XY: 0.177 AC XY: 13123 AN XY: 74340

African (AFR) AF: 0.166 AC: 6885 AN: 41476

American (AMR) AF: 0.174 AC: 2652 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 874 AN: 3472

East Asian (EAS) AF: 0.0891 AC: 462 AN: 5186

South Asian (SAS) AF: 0.195 AC: 939 AN: 4816

European-Finnish (FIN) AF: 0.165 AC: 1740 AN: 10556

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12632 AN: 67988

Other (OTH) AF: 0.208 AC: 440 AN: 2114

Alfa AF: 0.175 Hom.: 413

Bravo AF: 0.175

Asia WGS AF: 0.124 AC: 431 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.4
DANN	Benign	0.37
PhyloP100		0.74

Splicing

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

Other links and lift over

dbSNP: rs8042219; hg19: chr15-42352153;