chr17-43641975-G-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBP6_Very_Strong
The NM_004527.4(MEOX1):c.700C>A(p.Pro234Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00025 in 1,614,004 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0014 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00013 ( 1 hom. )
Consequence
MEOX1
NM_004527.4 missense
NM_004527.4 missense
Scores
3
5
8
Clinical Significance
Conservation
PhyloP100: 5.86
Genes affected
MEOX1 (HGNC:7013): (mesenchyme homeobox 1) This gene encodes a member of a subfamily of non-clustered, diverged, antennapedia-like homeobox-containing genes. The encoded protein may play a role in the molecular signaling network regulating somite development. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.005194038).
BP6
?
Variant 17-43641975-G-T is Benign according to our data. Variant chr17-43641975-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 736085.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MEOX1 | NM_004527.4 | c.700C>A | p.Pro234Thr | missense_variant | 3/3 | ENST00000318579.9 | |
MEOX1 | NM_013999.4 | c.527C>A | p.Ala176Asp | missense_variant | 2/2 | ||
MEOX1 | NM_001040002.2 | c.355C>A | p.Pro119Thr | missense_variant | 4/4 | ||
MEOX1 | XM_011524818.3 | c.*27C>A | 3_prime_UTR_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MEOX1 | ENST00000318579.9 | c.700C>A | p.Pro234Thr | missense_variant | 3/3 | 1 | NM_004527.4 | P1 | |
MEOX1 | ENST00000549132.2 | c.527C>A | p.Ala176Asp | missense_variant | 2/2 | 1 | |||
MEOX1 | ENST00000393661.2 | c.355C>A | p.Pro119Thr | missense_variant | 4/4 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00137 AC: 209AN: 152146Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.000433 AC: 108AN: 249468Hom.: 1 AF XY: 0.000319 AC XY: 43AN XY: 134984
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GnomAD4 exome AF: 0.000133 AC: 194AN: 1461740Hom.: 1 Cov.: 31 AF XY: 0.000114 AC XY: 83AN XY: 727178
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GnomAD4 genome ? AF: 0.00138 AC: 210AN: 152264Hom.: 1 Cov.: 32 AF XY: 0.00129 AC XY: 96AN XY: 74460
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
MEOX1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 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
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 12, 2023 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T
M_CAP
Benign
D
MetaRNN
Benign
T
MetaSVM
Uncertain
D
MutationTaster
Benign
D;D;D;D
PROVEAN
Uncertain
D
REVEL
Benign
Sift
Pathogenic
D
Sift4G
Pathogenic
D
Vest4
MVP
ClinPred
T
GERP RS
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at