chr1-156075392-T-A

Variant names:

• chr1-156075392-T-A
• rs3814314
• NM_001093725.2:c.*1182A>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MEX3A	NM_001093725.2	c.*1182A>T		3_prime_UTR_variant	Exon 2 of 2	ENST00000532414.3	NP_001087194.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MEX3A	ENST00000532414.3	c.*1182A>T		3_prime_UTR_variant	Exon 2 of 2	1	NM_001093725.2	ENSP00000432845.1

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

African (AFR) AF: 0.00 AC: 0 AN: 6

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.236 AC: 33 AN: 140

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.237 AC: 18 AN: 76

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.241 AC: 13 AN: 54

Other (OTH) AF: 0.00 AC: 0 AN: 14

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

African (AFR) AF: 0.0429 AC: 1782 AN: 41506

American (AMR) AF: 0.153 AC: 2335 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 617 AN: 3468

East Asian (EAS) AF: 0.0651 AC: 337 AN: 5180

South Asian (SAS) AF: 0.0796 AC: 383 AN: 4810

European-Finnish (FIN) AF: 0.248 AC: 2613 AN: 10554

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.230 AC: 15615 AN: 67954

Other (OTH) AF: 0.170 AC: 360 AN: 2112

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
PhyloP100		-0.41
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.3
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3814314; hg19: chr1-156045183;