rs11633714

Variant names:

• chr15-49849832-G-A
• rs11633714

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 0.191 in 152,046 control chromosomes in the GnomAD database, including 3,329 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 0.19 (3329 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.209

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 (NFE) allele frequency at 95% confidence interval = 0.262 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: 0.191 AC: 29090 AN: 151928 Hom.: 3329 Cov.: 32

Gnomad AFR AF: 0.0779

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.0241

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.191 AC: 29087 AN: 152046 Hom.: 3329 Cov.: 32 AF XY: 0.188 AC XY: 13950 AN XY: 74326

Gnomad4 AFR AF: 0.0778

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.0241

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.266

Gnomad4 OTH AF: 0.210

Alfa AF: 0.217 Hom.: 528

Bravo AF: 0.182

Asia WGS AF: 0.0780 AC: 273 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	9.5
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11633714; hg19: chr15-50142029;