rs16948760

Variant names:

• chr15-94158202-G-A
• rs16948760

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 0.132 in 152,038 control chromosomes in the GnomAD database, including 1,684 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 0.13 (1684 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.237 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: 0.132 AC: 20065 AN: 151920 Hom.: 1678 Cov.: 32

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.0990

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.0466

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.0423

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0934

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.132 AC: 20103 AN: 152038 Hom.: 1684 Cov.: 32 AF XY: 0.128 AC XY: 9495 AN XY: 74320

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.0988

Gnomad4 ASJ AF: 0.142

Gnomad4 EAS AF: 0.0467

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.0423

Gnomad4 NFE AF: 0.0934

Gnomad4 OTH AF: 0.134

Alfa AF: 0.102 Hom.: 931

Bravo AF: 0.140

Asia WGS AF: 0.0790 AC: 275 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.6
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16948760; hg19: chr15-94701431;