dbSNP rs1050582: MEST:c.*46G>C (chr7-130505102-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_002402.4(MEST):c.*46G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.532 in 1,357,274 control chromosomes in the GnomAD database, including 196,551 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 0.47 ( 18255 hom., cov: 32)

Exomes 𝑓: 0.54 ( 178296 hom. )

Consequence

MEST
NM_002402.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0170

Publications

10 publications found

Variant links:

Genes affected

MEST (HGNC:7028): (mesoderm specific transcript) This gene encodes a member of the alpha/beta hydrolase superfamily. It is imprinted, exhibiting preferential expression from the paternal allele in fetal tissues, and isoform-specific imprinting in lymphocytes. The loss of imprinting of this gene has been linked to certain types of cancer and may be due to promotor switching. The encoded protein may play a role in development. Alternatively spliced transcript variants encoding multiple isoforms have been identified for this gene. Pseudogenes of this gene are located on the short arm of chromosomes 3 and 4, and the long arm of chromosomes 6 and 15. [provided by RefSeq, Dec 2011]

MEST 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=-0.73).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MEST	NM_002402.4 link	c.*46G>C		3_prime_UTR_variant	Exon 12 of 12	ENST00000223215.10	NP_002393.2	Q5EB52-1A0A024R768

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MEST	ENST00000223215.10 link	c.*46G>C		3_prime_UTR_variant	Exon 12 of 12	1	NM_002402.4	ENSP00000223215.4		Q5EB52-1

Frequencies

GnomAD3 genomes

AF:

0.472

AC:

71642

AN:

151930

Hom.:

18240

Cov.:

show subpopulations

Gnomad AFR

AF:

0.267

Gnomad AMI

AF:

0.462

Gnomad AMR

AF:

0.537

Gnomad ASJ

AF:

0.539

Gnomad EAS

AF:

0.594

Gnomad SAS

AF:

0.495

Gnomad FIN

AF:

0.564

Gnomad MID

AF:

0.434

Gnomad NFE

AF:

0.552

Gnomad OTH

AF:

0.482

GnomAD2 exomes

AF:

0.525

AC:

130355

AN:

248060

AF XY:

0.525

show subpopulations

Gnomad AFR exome

AF:

0.257

Gnomad AMR exome

AF:

0.545

Gnomad ASJ exome

AF:

0.523

Gnomad EAS exome

AF:

0.595

Gnomad FIN exome

AF:

0.563

Gnomad NFE exome

AF:

0.550

Gnomad OTH exome

AF:

0.522

GnomAD4 exome

AF:

0.540

AC:

650313

AN:

1205226

Hom.:

178296

Cov.:

AF XY:

0.538

AC XY:

328968

AN XY:

611834

show subpopulations

African (AFR)

AF:

0.261

AC:

7414

AN:

28426

American (AMR)

AF:

0.545

AC:

24064

AN:

44180

Ashkenazi Jewish (ASJ)

AF:

0.519

AC:

12634

AN:

24364

East Asian (EAS)

AF:

0.608

AC:

23373

AN:

38440

South Asian (SAS)

AF:

0.487

AC:

39354

AN:

80850

European-Finnish (FIN)

AF:

0.563

AC:

29313

AN:

52064

Middle Eastern (MID)

AF:

0.377

AC:

1421

AN:

3768

European-Non Finnish (NFE)

AF:

0.551

AC:

485681

AN:

881406

Other (OTH)

AF:

0.523

AC:

27059

AN:

51728

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

13618

27235

40853

54470

68088

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.472

AC:

71695

AN:

152048

Hom.:

18255

Cov.:

AF XY:

0.474

AC XY:

35210

AN XY:

74290

show subpopulations

African (AFR)

AF:

0.268

AC:

11106

AN:

41468

American (AMR)

AF:

0.537

AC:

8206

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.539

AC:

1872

AN:

3472

East Asian (EAS)

AF:

0.594

AC:

3065

AN:

5158

South Asian (SAS)

AF:

0.496

AC:

2391

AN:

4822

European-Finnish (FIN)

AF:

0.564

AC:

5956

AN:

10556

Middle Eastern (MID)

AF:

0.466

AC:

137

AN:

294

European-Non Finnish (NFE)

AF:

0.552

AC:

37529

AN:

67970

Other (OTH)

AF:

0.480

AC:

1013

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1832

3664

5497

7329

9161

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.504

Hom.:

3710

Bravo

AF:

0.463

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

(source)

DANN

Benign

0.80

PhyloP100

0.017

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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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rs1050582

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