Variant chr15-89751050-A-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_018670.4(MESP1):c.182T>G(p.Leu61Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 1,317,352 control chromosomes in the GnomAD database, including 41,669 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.27 ( 5827 hom., cov: 34)

Exomes 𝑓: 0.24 ( 35842 hom. )

Consequence

MESP1
NM_018670.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -2.79

Variant links:

Genes affected

MESP1 (HGNC:29658): (mesoderm posterior bHLH transcription factor 1) Enables DNA-binding transcription factor activity and transcription cis-regulatory region binding activity. Involved in several processes, including endothelial cell differentiation; heart development; and positive regulation of transcription by RNA polymerase II. Predicted to be part of chromatin. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

MESP1 links:

MESP1 (HGNC:):

MESP1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.005183816).

BP6

Variant 15-89751050-A-C is Benign according to our data. Variant chr15-89751050-A-C is described in ClinVar as [Benign]. Clinvar id is 1548747.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr15-89751050-A-C is described in Lovd as [Likely_benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MESP1	NM_018670.4 linkuse as main transcript	c.182T>G	p.Leu61Arg	missense_variant	1/2	ENST00000300057.5	NP_061140.1	Q9BRJ9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MESP1	ENST00000300057.5 linkuse as main transcript	c.182T>G	p.Leu61Arg	missense_variant	1/2	1	NM_018670.4	ENSP00000300057.4		Q9BRJ9
MESP1	ENST00000559894.1 linkuse as main transcript	n.88T>G		non_coding_transcript_exon_variant	1/2	2

Frequencies

GnomAD3 genomes

AF:

0.269

AC:

40639

AN:

151196

Hom.:

5821

Cov.:

show subpopulations

Gnomad AFR

AF:

0.370

Gnomad AMI

AF:

0.481

Gnomad AMR

AF:

0.209

Gnomad ASJ

AF:

0.243

Gnomad EAS

AF:

0.123

Gnomad SAS

AF:

0.288

Gnomad FIN

AF:

0.147

Gnomad MID

AF:

0.221

Gnomad NFE

AF:

0.249

Gnomad OTH

AF:

0.250

GnomAD3 exomes

AF:

0.0267

AC:

218

AN:

8172

Hom.:

AF XY:

0.0268

AC XY:

124

AN XY:

4620

show subpopulations

Gnomad AFR exome

AF:

0.0907

Gnomad AMR exome

AF:

0.00690

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00643

Gnomad SAS exome

AF:

0.0271

Gnomad FIN exome

AF:

0.00645

Gnomad NFE exome

AF:

0.0286

Gnomad OTH exome

AF:

0.0156

GnomAD4 exome

AF:

0.242

AC:

281777

AN:

1166050

Hom.:

35842

Cov.:

AF XY:

0.239

AC XY:

134631

AN XY:

562464

show subpopulations

Gnomad4 AFR exome

AF:

0.365

Gnomad4 AMR exome

AF:

0.172

Gnomad4 ASJ exome

AF:

0.221

Gnomad4 EAS exome

AF:

0.147

Gnomad4 SAS exome

AF:

0.204

Gnomad4 FIN exome

AF:

0.143

Gnomad4 NFE exome

AF:

0.247

Gnomad4 OTH exome

AF:

0.238

GnomAD4 genome

AF:

0.269

AC:

40667

AN:

151302

Hom.:

5827

Cov.:

AF XY:

0.262

AC XY:

19362

AN XY:

73958

show subpopulations

Gnomad4 AFR

AF:

0.370

Gnomad4 AMR

AF:

0.209

Gnomad4 ASJ

AF:

0.243

Gnomad4 EAS

AF:

0.123

Gnomad4 SAS

AF:

0.287

Gnomad4 FIN

AF:

0.147

Gnomad4 NFE

AF:

0.249

Gnomad4 OTH

AF:

0.247

Alfa

AF:

0.257

Hom.:

629

Bravo

AF:

0.273

ExAC

AF:

0.0179

AC:

1401

Asia WGS

AF:

0.211

AC:

731

AN:

3452

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -

MESP1-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Nov 11, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.042

BayesDel_addAF

Benign

-0.66

BayesDel_noAF

Benign

-0.58

CADD

Benign

0.37

DANN

Benign

0.24

DEOGEN2

Benign

0.089

Eigen

Benign

-1.6

Eigen_PC

Benign

-1.6

FATHMM_MKL

Benign

0.011

LIST_S2

Benign

0.16

MetaRNN

Benign

0.0052

MetaSVM

Benign

-1.0

MutationAssessor

Benign

-0.69

PrimateAI

Uncertain

0.74

PROVEAN

Benign

0.32

REVEL

Benign

0.097

Sift

Benign

0.48

Sift4G

Benign

0.45

Polyphen

0.0

Vest4

0.028

MPC

0.65

ClinPred

0.0040

GERP RS

-1.6

Varity_R

0.080

gMVP

0.22

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over