rs3814314

Positions:

• chr1-156075392-T-A

Variant summary

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

The NM_001093725.2(MEX3A):​c.*1182A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 152,360 control chromosomes in the GnomAD database, including 2,560 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 0.16 (2554 hom., cov: 31)
  • Exomes 𝑓: 0.22 (6 hom.)
• Consequence: MEX3A NM_001093725.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.411

Genes affected

MEX3A (HGNC:33482): (mex-3 RNA binding family member A) Enables RNA binding activity. Located in P-body and cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.227 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MEX3A	NM_001093725.2	c.*1182A>T		3_prime_UTR_variant	2/2	ENST00000532414.3	NP_001087194.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MEX3A	ENST00000532414.3	c.*1182A>T		3_prime_UTR_variant	2/2	1	NM_001093725.2	ENSP00000432845	P1

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24461 AN: 151950 Hom.: 2554 Cov.: 31

Gnomad AFR AF: 0.0431

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.0649

Gnomad SAS AF: 0.0794

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.172

GnomAD4 exome AF: 0.219 AC: 64 AN: 292 Hom.: 6 Cov.: 0 AF XY: 0.227 AC XY: 40 AN XY: 176

Gnomad4 AFR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.236

Gnomad4 FIN exome AF: 0.237

Gnomad4 NFE exome AF: 0.241

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.161 AC: 24456 AN: 152068 Hom.: 2554 Cov.: 31 AF XY: 0.160 AC XY: 11911 AN XY: 74320

Gnomad4 AFR AF: 0.0429

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.0651

Gnomad4 SAS AF: 0.0796

Gnomad4 FIN AF: 0.248

Gnomad4 NFE AF: 0.230

Gnomad4 OTH AF: 0.170

Alfa AF: 0.194 Hom.: 440

Bravo AF: 0.152

Asia WGS AF: 0.0690 AC: 239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	12
DANN	Benign	0.87
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs3814314; hg19: chr1-156045183;