rs11858157

Positions:

• chr15-91852168-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 0.249 in 151,990 control chromosomes in the GnomAD database, including 5,228 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 0.25 (5228 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.570

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37837 AN: 151872 Hom.: 5219 Cov.: 32

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.0181

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.249 AC: 37880 AN: 151990 Hom.: 5228 Cov.: 32 AF XY: 0.243 AC XY: 18065 AN XY: 74322

Gnomad4 AFR AF: 0.368

Gnomad4 AMR AF: 0.219

Gnomad4 ASJ AF: 0.252

Gnomad4 EAS AF: 0.0184

Gnomad4 SAS AF: 0.108

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.223

Gnomad4 OTH AF: 0.242

Alfa AF: 0.233 Hom.: 906

Bravo AF: 0.258

Asia WGS AF: 0.0960 AC: 338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.0
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: rs11858157; hg19: chr15-92395398;