rs1503351

Variant names:

• chr15-96814290-A-G
• rs1503351

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 0.0453 in 152,220 control chromosomes in the GnomAD database, including 186 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 0.045 (186 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.677
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0534 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: 0.0454 AC: 6898 AN: 152102 Hom.: 185 Cov.: 32

Gnomad AFR AF: 0.0553

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.0336

Gnomad ASJ AF: 0.0499

Gnomad EAS AF: 0.0324

Gnomad SAS AF: 0.0201

Gnomad FIN AF: 0.0470

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0442

Gnomad OTH AF: 0.0407

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

GnomAD4 genome AF: 0.0453 AC: 6901 AN: 152220 Hom.: 186 Cov.: 32 AF XY: 0.0445 AC XY: 3311 AN XY: 74416

African (AFR) AF: 0.0553 AC: 2295 AN: 41538

American (AMR) AF: 0.0336 AC: 513 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0499 AC: 173 AN: 3468

East Asian (EAS) AF: 0.0324 AC: 168 AN: 5180

South Asian (SAS) AF: 0.0199 AC: 96 AN: 4816

European-Finnish (FIN) AF: 0.0470 AC: 498 AN: 10600

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0442 AC: 3004 AN: 68012

Other (OTH) AF: 0.0402 AC: 85 AN: 2112

Alfa AF: 0.0454 Hom.: 19

Bravo AF: 0.0458

Asia WGS AF: 0.0250 AC: 85 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.5
DANN	Benign	0.71
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs1503351; hg19: chr15-97357520;