rs11634947

Positions:

• chr15-49705019-C-G
• chr15-49705019-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 0.255 in 152,076 control chromosomes in the GnomAD database, including 5,954 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 0.26 (5954 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.432

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.35 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: 0.255 AC: 38810 AN: 151958 Hom.: 5954 Cov.: 33

Gnomad AFR AF: 0.0862

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.255 AC: 38795 AN: 152076 Hom.: 5954 Cov.: 33 AF XY: 0.252 AC XY: 18728 AN XY: 74322

Gnomad4 AFR AF: 0.0860

Gnomad4 AMR AF: 0.251

Gnomad4 ASJ AF: 0.355

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.290

Gnomad4 NFE AF: 0.353

Gnomad4 OTH AF: 0.271

Alfa AF: 0.287 Hom.: 886

Bravo AF: 0.243

Asia WGS AF: 0.183 AC: 637 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11634947; hg19: chr15-49997216;