rs1873147

Positions:

• chr15-63020433-G-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;