rs16960538

chr15-48077288-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 0.0444 in 152,284 control chromosomes in the GnomAD database, including 341 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 0.044 (341 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.269 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: 0.0443 AC: 6746 AN: 152166 Hom.: 342 Cov.: 32

Gnomad AFR AF: 0.0231

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0773

Gnomad ASJ AF: 0.00922

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.0441

Gnomad FIN AF: 0.0318

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0357

Gnomad OTH AF: 0.0493

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

GnomAD4 genome AF: 0.0444 AC: 6754 AN: 152284 Hom.: 341 Cov.: 32 AF XY: 0.0465 AC XY: 3462 AN XY: 74452

Gnomad4 AFR AF: 0.0232

Gnomad4 AMR AF: 0.0775

Gnomad4 ASJ AF: 0.00922

Gnomad4 EAS AF: 0.281

Gnomad4 SAS AF: 0.0444

Gnomad4 FIN AF: 0.0318

Gnomad4 NFE AF: 0.0357

Gnomad4 OTH AF: 0.0497

Alfa AF: 0.0360 Hom.: 16

Bravo AF: 0.0509

Asia WGS AF: 0.151 AC: 523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	5.6
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16960538; hg19: chr15-48369485;