rs1370176

Variant names:

• chr15-62105035-G-A
• rs1370176

Your query was ambiguous. Multiple possible variants found:

• chr15-62105035-G-A
• chr15-62105035-G-C

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 0.307 in 151,956 control chromosomes in the GnomAD database, including 8,087 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 0.31 (8087 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.799
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.466 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: 0.307 AC: 46618 AN: 151838 Hom.: 8058 Cov.: 32

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.307 AC: 46704 AN: 151956 Hom.: 8087 Cov.: 32 AF XY: 0.309 AC XY: 22922 AN XY: 74244

African (AFR) AF: 0.472 AC: 19559 AN: 41438

American (AMR) AF: 0.259 AC: 3960 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 615 AN: 3472

East Asian (EAS) AF: 0.282 AC: 1453 AN: 5144

South Asian (SAS) AF: 0.209 AC: 1006 AN: 4812

European-Finnish (FIN) AF: 0.341 AC: 3596 AN: 10546

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.230 AC: 15617 AN: 67954

Other (OTH) AF: 0.288 AC: 608 AN: 2114

Alfa AF: 0.248 Hom.: 21606

Bravo AF: 0.309

Asia WGS AF: 0.298 AC: 1034 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.30
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs1370176; hg19: chr15-62397234;