rs715774

Variant names:

• chr15-69910520-G-A
• rs715774

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 0.189 in 152,110 control chromosomes in the GnomAD database, including 3,093 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 0.19 (3093 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.239 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: 0.190 AC: 28818 AN: 151992 Hom.: 3094 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.00733

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.189 AC: 28824 AN: 152110 Hom.: 3093 Cov.: 32 AF XY: 0.185 AC XY: 13793 AN XY: 74356

African (AFR) AF: 0.124 AC: 5142 AN: 41490

American (AMR) AF: 0.166 AC: 2530 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 735 AN: 3470

East Asian (EAS) AF: 0.00715 AC: 37 AN: 5174

South Asian (SAS) AF: 0.231 AC: 1113 AN: 4820

European-Finnish (FIN) AF: 0.181 AC: 1909 AN: 10568

Middle Eastern (MID) AF: 0.236 AC: 69 AN: 292

European-Non Finnish (NFE) AF: 0.242 AC: 16472 AN: 67992

Other (OTH) AF: 0.208 AC: 439 AN: 2114

Alfa AF: 0.215 Hom.: 2123

Bravo AF: 0.183

Asia WGS AF: 0.126 AC: 437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.1
DANN	Benign	0.68
PhyloP100		-0.049

Splicing

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

Other links and lift over

dbSNP: rs715774; hg19: chr15-70202859;