rs2119547

chr18-50437594-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 0.11 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;