rs919129

Variant names:

• chr15-48383030-G-A
• rs919129

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 0.759 in 152,210 control chromosomes in the GnomAD database, including 45,457 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 0.76 (45457 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.843 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: 0.759 AC: 115418 AN: 152092 Hom.: 45438 Cov.: 33

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.942

Gnomad AMR AF: 0.831

Gnomad ASJ AF: 0.833

Gnomad EAS AF: 0.856

Gnomad SAS AF: 0.803

Gnomad FIN AF: 0.862

Gnomad MID AF: 0.809

Gnomad NFE AF: 0.849

Gnomad OTH AF: 0.775

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

GnomAD4 genome AF: 0.759 AC: 115489 AN: 152210 Hom.: 45457 Cov.: 33 AF XY: 0.763 AC XY: 56795 AN XY: 74424

Gnomad4 AFR AF: 0.529

Gnomad4 AMR AF: 0.831

Gnomad4 ASJ AF: 0.833

Gnomad4 EAS AF: 0.857

Gnomad4 SAS AF: 0.806

Gnomad4 FIN AF: 0.862

Gnomad4 NFE AF: 0.849

Gnomad4 OTH AF: 0.776

Alfa AF: 0.827 Hom.: 69338

Bravo AF: 0.751

Asia WGS AF: 0.824 AC: 2866 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.2
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs919129; hg19: chr15-48675227;