rs1503351

chr15-96814290-A-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0553

Gnomad4 AMR AF: 0.0336

Gnomad4 ASJ AF: 0.0499

Gnomad4 EAS AF: 0.0324

Gnomad4 SAS AF: 0.0199

Gnomad4 FIN AF: 0.0470

Gnomad4 NFE AF: 0.0442

Gnomad4 OTH AF: 0.0402

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1503351; hg19: chr15-97357520;