Genetic Variant NM_001093725.2:c.*1182A>T (chr1-156075392-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.411

Publications

5 publications found

Variant links:

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]

MEX3A links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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 link	c.*1182A>T		3_prime_UTR_variant	Exon 2 of 2	ENST00000532414.3	NP_001087194.1	A1L020

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MEX3A	ENST00000532414.3 link	c.*1182A>T		3_prime_UTR_variant	Exon 2 of 2	1	NM_001093725.2	ENSP00000432845.1		A1L020

Frequencies

GnomAD3 genomes

AF:

0.161

AC:

24461

AN:

151950

Hom.:

2554

Cov.:

show subpopulations

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:

AN:

292

Hom.:

Cov.:

AF XY:

0.227

AC XY:

AN XY:

176

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.236

AC:

AN:

140

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.237

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.241

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.466

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.161

AC:

24456

AN:

152068

Hom.:

2554

Cov.:

AF XY:

0.160

AC XY:

11911

AN XY:

74320

show subpopulations

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.230

AC:

15615

AN:

67954

Other (OTH)

AF:

0.170

AC:

360

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1001

2002

3003

4004

5005

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

256

512

768

1024

1280

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

(source)

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)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over