rs16960538

Variant names:

• chr15-48077288-A-G
• rs16960538

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;