rs896588

Variant names:

• chr15-73813152-A-G
• rs896588

Variant summary

Our verdict is Benign. The variant received -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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.100
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.822 AC: 34115 AN: 41510

American (AMR) AF: 0.823 AC: 12581 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.830 AC: 2882 AN: 3472

East Asian (EAS) AF: 0.754 AC: 3875 AN: 5136

South Asian (SAS) AF: 0.667 AC: 3210 AN: 4812

European-Finnish (FIN) AF: 0.707 AC: 7461 AN: 10558

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.776 AC: 52794 AN: 67990

Other (OTH) AF: 0.792 AC: 1672 AN: 2110

Alfa AF: 0.784 Hom.: 200488

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
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs896588; hg19: chr15-74105493;