rs2119547

Variant names:

• chr18-50437594-C-T
• rs2119547

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 0.11 in 152,268 control chromosomes in the GnomAD database, including 960 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 0.11 (960 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.329

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.124 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: 0.110 AC: 16767 AN: 152150 Hom.: 957 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.0804

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.0829

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.110 AC: 16780 AN: 152268 Hom.: 960 Cov.: 32 AF XY: 0.110 AC XY: 8177 AN XY: 74446

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.111

Gnomad4 EAS AF: 0.0806

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.0829

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.125

Alfa AF: 0.108 Hom.: 744

Bravo AF: 0.113

Asia WGS AF: 0.116 AC: 402 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.7
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2119547; hg19: chr18-47963964;