chr18-51192166-G-A

Variant names:

• chr18-51192166-G-A
• rs1893379
• NM_016626.5:c.754+4401C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016626.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MEX3C	NM_016626.5	MANE Select	c.754+4401C>T		intron	N/A	NP_057710.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MEX3C	ENST00000406189.4	TSL:1 MANE Select	c.754+4401C>T		intron	N/A	ENSP00000385610.3
	MEX3C	ENST00000591040.2	TSL:2	c.-107-14590C>T		intron	N/A	ENSP00000502049.1

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

African (AFR) AF: 0.192 AC: 7960 AN: 41394

American (AMR) AF: 0.356 AC: 5437 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.460 AC: 1595 AN: 3468

East Asian (EAS) AF: 0.234 AC: 1209 AN: 5168

South Asian (SAS) AF: 0.354 AC: 1705 AN: 4812

European-Finnish (FIN) AF: 0.421 AC: 4430 AN: 10512

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.451 AC: 30625 AN: 67860

Other (OTH) AF: 0.367 AC: 775 AN: 2110

Alfa AF: 0.276 Hom.: 816

Bravo AF: 0.341

Asia WGS AF: 0.262 AC: 908 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	10
DANN	Benign	0.49
PhyloP100		0.63
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1893379; hg19: chr18-48718536;