ENST00000591040.2:c.-108+17756T>C

Variant names:

• chr18-51200506-A-G
• rs1941958
• ENST00000591040.2:c.-108+17756T>C

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MEX3C	ENST00000591040.2	c.-108+17756T>C		intron_variant	Intron 1 of 1	2		ENSP00000502049.1

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;