rs2542151

Variant names:

• chr18-12779948-G-T
• rs2542151

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.831 in 152,208 control chromosomes in the GnomAD database, including 52,673 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 0.83 (52673 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.436

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.845 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: 0.831 AC: 126378 AN: 152090 Hom.: 52623 Cov.: 32

Gnomad AFR AF: 0.792

Gnomad AMI AF: 0.954

Gnomad AMR AF: 0.858

Gnomad ASJ AF: 0.906

Gnomad EAS AF: 0.833

Gnomad SAS AF: 0.813

Gnomad FIN AF: 0.861

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.839

Gnomad OTH AF: 0.844

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

GnomAD4 genome AF: 0.831 AC: 126486 AN: 152208 Hom.: 52673 Cov.: 32 AF XY: 0.831 AC XY: 61863 AN XY: 74426

Gnomad4 AFR AF: 0.792 AC: 0.792371 AN: 0.792371

Gnomad4 AMR AF: 0.857 AC: 0.857348 AN: 0.857348

Gnomad4 ASJ AF: 0.906 AC: 0.90634 AN: 0.90634

Gnomad4 EAS AF: 0.832 AC: 0.832043 AN: 0.832043

Gnomad4 SAS AF: 0.814 AC: 0.8139 AN: 0.8139

Gnomad4 FIN AF: 0.861 AC: 0.860524 AN: 0.860524

Gnomad4 NFE AF: 0.839 AC: 0.839064 AN: 0.839064

Gnomad4 OTH AF: 0.846 AC: 0.845936 AN: 0.845936

Alfa AF: 0.839 Hom.: 165824

Bravo AF: 0.831

Asia WGS AF: 0.816 AC: 2839 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.47
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2542151; hg19: chr18-12779947;