rs1893378

Positions:

• chr18-51192490-G-A

Variant summary

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

The NM_016626.5(MEX3C):​c.754+4077C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.502 in 151,898 control chromosomes in the GnomAD database, including 19,263 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 0.50 (19263 hom., cov: 33)
• Consequence: MEX3C NM_016626.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.288

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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.53 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MEX3C	NM_016626.5	c.754+4077C>T		intron_variant		ENST00000406189.4	NP_057710.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MEX3C	ENST00000406189.4	c.754+4077C>T		intron_variant		1	NM_016626.5	ENSP00000385610.3
MEX3C	ENST00000591040.2	c.-107-14914C>T		intron_variant		2		ENSP00000502049.1

Frequencies

GnomAD3 genomes AF: 0.502 AC: 76144 AN: 151780 Hom.: 19247 Cov.: 33

Gnomad AFR AF: 0.483

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.534

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.502 AC: 76211 AN: 151898 Hom.: 19263 Cov.: 33 AF XY: 0.496 AC XY: 36846 AN XY: 74254

Gnomad4 AFR AF: 0.484

Gnomad4 AMR AF: 0.454

Gnomad4 ASJ AF: 0.531

Gnomad4 EAS AF: 0.433

Gnomad4 SAS AF: 0.447

Gnomad4 FIN AF: 0.486

Gnomad4 NFE AF: 0.534

Gnomad4 OTH AF: 0.498

Alfa AF: 0.524 Hom.: 2571

Bravo AF: 0.494

Asia WGS AF: 0.427 AC: 1481 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.4
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1893378; hg19: chr18-48718860;