rs1873147

Variant names:

• chr15-63020433-G-A
• rs1873147

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 0.653 in 152,064 control chromosomes in the GnomAD database, including 33,733 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 0.65 (33733 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0660

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.725 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: 0.654 AC: 99322 AN: 151946 Hom.: 33722 Cov.: 32

Gnomad AFR AF: 0.570

Gnomad AMI AF: 0.858

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.809

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.731

Gnomad OTH AF: 0.697

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

GnomAD4 genome AF: 0.653 AC: 99373 AN: 152064 Hom.: 33733 Cov.: 32 AF XY: 0.646 AC XY: 48054 AN XY: 74340

Gnomad4 AFR AF: 0.570

Gnomad4 AMR AF: 0.673

Gnomad4 ASJ AF: 0.809

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.485

Gnomad4 FIN AF: 0.708

Gnomad4 NFE AF: 0.731

Gnomad4 OTH AF: 0.693

Alfa AF: 0.713 Hom.: 67778

Bravo AF: 0.651

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.6
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1873147; hg19: chr15-63312632;