rs11853883

Positions:

• chr15-94176687-G-A
• chr15-94176687-G-T

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 0.296 in 152,002 control chromosomes in the GnomAD database, including 6,943 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 0.30 (6943 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0690

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.569 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: 0.296 AC: 44913 AN: 151884 Hom.: 6937 Cov.: 31

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.296 AC: 44938 AN: 152002 Hom.: 6943 Cov.: 31 AF XY: 0.294 AC XY: 21828 AN XY: 74312

Gnomad4 AFR AF: 0.288

Gnomad4 AMR AF: 0.336

Gnomad4 ASJ AF: 0.364

Gnomad4 EAS AF: 0.587

Gnomad4 SAS AF: 0.235

Gnomad4 FIN AF: 0.217

Gnomad4 NFE AF: 0.279

Gnomad4 OTH AF: 0.320

Alfa AF: 0.274 Hom.: 4666

Bravo AF: 0.310

Asia WGS AF: 0.369 AC: 1283 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.2
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11853883; hg19: chr15-94719916;