rs896588

Positions:

• chr15-73813152-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 0.786 in 152,084 control chromosomes in the GnomAD database, including 47,147 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 0.79 (47147 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.100

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.73813152A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.786 AC: 119425 AN: 151966 Hom.: 47102 Cov.: 31

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.823

Gnomad ASJ AF: 0.830

Gnomad EAS AF: 0.755

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.707

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.777

Gnomad OTH AF: 0.792

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

GnomAD4 genome AF: 0.786 AC: 119527 AN: 152084 Hom.: 47147 Cov.: 31 AF XY: 0.782 AC XY: 58141 AN XY: 74342

Gnomad4 AFR AF: 0.822

Gnomad4 AMR AF: 0.823

Gnomad4 ASJ AF: 0.830

Gnomad4 EAS AF: 0.754

Gnomad4 SAS AF: 0.667

Gnomad4 FIN AF: 0.707

Gnomad4 NFE AF: 0.776

Gnomad4 OTH AF: 0.792

Alfa AF: 0.784 Hom.: 94513

Bravo AF: 0.798

Asia WGS AF: 0.744 AC: 2587 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.8
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs896588; hg19: chr15-74105493;