chr15-89750192-G-C
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_018670.4(MESP1):āc.759C>Gā(p.Thr253=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000762 in 1,614,096 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Genomes: š 0.000092 ( 0 hom., cov: 33)
Exomes š: 0.000075 ( 1 hom. )
Consequence
MESP1
NM_018670.4 synonymous
NM_018670.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.28
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.58).
BP6
Variant 15-89750192-G-C is Benign according to our data. Variant chr15-89750192-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 2049052.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=2.28 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MESP1 | NM_018670.4 | c.759C>G | p.Thr253= | synonymous_variant | 2/2 | ENST00000300057.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MESP1 | ENST00000300057.5 | c.759C>G | p.Thr253= | synonymous_variant | 2/2 | 1 | NM_018670.4 | P1 | |
MESP1 | ENST00000559894.1 | n.150C>G | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152230Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000257 AC: 64AN: 248866Hom.: 0 AF XY: 0.000260 AC XY: 35AN XY: 134756
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GnomAD4 exome AF: 0.0000746 AC: 109AN: 1461748Hom.: 1 Cov.: 31 AF XY: 0.0000729 AC XY: 53AN XY: 727182
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GnomAD4 genome AF: 0.0000919 AC: 14AN: 152348Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74492
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
MESP1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 20, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 05, 2022 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at