rs1941958

chr18-51200506-A-Gchr18-51200506-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000591040.2(MEX3C):c.-108+17756T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 151,992 control chromosomes in the GnomAD database, including 20,331 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 0.52 (20331 hom., cov: 32)
• Consequence: MEX3C ENST00000591040.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.329

Genes affected

MEX3C (HGNC:28040): (mex-3 RNA binding family member C) This gene encodes a member of a family of proteins with two K homology (KH) RNA-binding domains and a C-terminal RING-finger domain. The protein interacts with mRNA via the KH domains, and the protein shuttles between the nucleus and cytoplasm. Polymorphisms in this gene may contribute to hypertension. [provided by RefSeq, Oct 2009]

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 = 0.532 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
MEX3C	ENST00000591040.2	c.-108+17756T>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.516 AC: 78295 AN: 151874 Hom.: 20312 Cov.: 32

Gnomad AFR AF: 0.538

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.505

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

GnomAD4 genome AF: 0.516 AC: 78363 AN: 151992 Hom.: 20331 Cov.: 32 AF XY: 0.510 AC XY: 37904 AN XY: 74296

Gnomad4 AFR AF: 0.538

Gnomad4 AMR AF: 0.454

Gnomad4 ASJ AF: 0.518

Gnomad4 EAS AF: 0.431

Gnomad4 SAS AF: 0.446

Gnomad4 FIN AF: 0.484

Gnomad4 NFE AF: 0.533

Gnomad4 OTH AF: 0.503

Alfa AF: 0.517 Hom.: 18966

Bravo AF: 0.511

Asia WGS AF: 0.431 AC: 1498 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	0.65
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: rs1941958; hg19: chr18-48726876;