rs1893379

Positions:

• chr18-51192166-G-A
• chr18-51192166-G-C
• chr18-51192166-G-T

Variant summary

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

The NM_016626.5(MEX3C):​c.754+4401C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 151,794 control chromosomes in the GnomAD database, including 10,778 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 0.36 (10778 hom., cov: 31)
• Consequence: MEX3C NM_016626.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.634

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=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MEX3C	NM_016626.5	c.754+4401C>T		intron_variant		ENST00000406189.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MEX3C	ENST00000406189.4	c.754+4401C>T		intron_variant		1	NM_016626.5	P1
MEX3C	ENST00000591040.2	c.-107-14590C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54159 AN: 151674 Hom.: 10782 Cov.: 31

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.357 AC: 54161 AN: 151794 Hom.: 10778 Cov.: 31 AF XY: 0.354 AC XY: 26285 AN XY: 74202

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.356

Gnomad4 ASJ AF: 0.460

Gnomad4 EAS AF: 0.234

Gnomad4 SAS AF: 0.354

Gnomad4 FIN AF: 0.421

Gnomad4 NFE AF: 0.451

Gnomad4 OTH AF: 0.367

Alfa AF: 0.281 Hom.: 796

Bravo AF: 0.341

Asia WGS AF: 0.262 AC: 908 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	10
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1893379; hg19: chr18-48718536;