rs11952141

Variant names:

• chr5-18024691-A-G
• rs11952141

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 0.184 in 152,038 control chromosomes in the GnomAD database, including 3,585 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 0.18 (3585 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.32

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.348 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: 0.183 AC: 27853 AN: 151920 Hom.: 3565 Cov.: 32

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.0658

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.0890

Gnomad MID AF: 0.102

Gnomad NFE AF: 0.0985

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.184 AC: 27919 AN: 152038 Hom.: 3585 Cov.: 32 AF XY: 0.182 AC XY: 13499 AN XY: 74338

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.0658

Gnomad4 EAS AF: 0.249

Gnomad4 SAS AF: 0.158

Gnomad4 FIN AF: 0.0890

Gnomad4 NFE AF: 0.0985

Gnomad4 OTH AF: 0.155

Alfa AF: 0.135 Hom.: 472

Bravo AF: 0.198

Asia WGS AF: 0.214 AC: 745 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.24
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11952141; hg19: chr5-18024800;