rs11857194

chr15-66697177-C-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 0.233 in 152,026 control chromosomes in the GnomAD database, including 4,161 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 0.23 (4161 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46

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 (NFE) allele frequency at 95% confidence interval = 0.251 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: 0.233 AC: 35417 AN: 151908 Hom.: 4163 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.233 AC: 35421 AN: 152026 Hom.: 4161 Cov.: 32 AF XY: 0.230 AC XY: 17086 AN XY: 74314

Gnomad4 AFR AF: 0.227

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.210

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.236

Alfa AF: 0.254 Hom.: 7791

Bravo AF: 0.231

Asia WGS AF: 0.185 AC: 642 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.091
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11857194; hg19: chr15-66989515;