15-48401585-G-A

Variant names:

• chr15-48401585-G-A
• rs16960880

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 0.0591 in 152,088 control chromosomes in the GnomAD database, including 305 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 0.059 (305 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.709
• Publications: 5 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 (EAS) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0591 AC: 8982 AN: 151970 Hom.: 304 Cov.: 32

Gnomad AFR AF: 0.0525

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.0610

Gnomad ASJ AF: 0.0429

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.0946

Gnomad FIN AF: 0.0745

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0514

Gnomad OTH AF: 0.0632

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

GnomAD4 genome AF: 0.0591 AC: 8985 AN: 152088 Hom.: 305 Cov.: 32 AF XY: 0.0599 AC XY: 4451 AN XY: 74340

African (AFR) AF: 0.0525 AC: 2177 AN: 41482

American (AMR) AF: 0.0610 AC: 931 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0429 AC: 149 AN: 3472

East Asian (EAS) AF: 0.156 AC: 807 AN: 5174

South Asian (SAS) AF: 0.0928 AC: 445 AN: 4794

European-Finnish (FIN) AF: 0.0745 AC: 789 AN: 10584

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0514 AC: 3493 AN: 67994

Other (OTH) AF: 0.0687 AC: 145 AN: 2110

Alfa AF: 0.0558 Hom.: 78

Bravo AF: 0.0579

Asia WGS AF: 0.160 AC: 554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.72
DANN	Benign	0.62
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs16960880; hg19: chr15-48693782;