rs16960880

chr15-48401585-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 0.0591 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

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 (EAS) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

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

Gnomad4 AFR AF: 0.0525

Gnomad4 AMR AF: 0.0610

Gnomad4 ASJ AF: 0.0429

Gnomad4 EAS AF: 0.156

Gnomad4 SAS AF: 0.0928

Gnomad4 FIN AF: 0.0745

Gnomad4 NFE AF: 0.0514

Gnomad4 OTH AF: 0.0687

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.72
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16960880; hg19: chr15-48693782;