X-150731590-G-T
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_001306144.3(MTMR1):c.862G>T(p.Ala288Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000499 in 1,203,287 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 16 hemizygotes in GnomAD. 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 0.0000089 ( 0 hom., 1 hem., cov: 23)
Exomes 𝑓: 0.000054 ( 0 hom. 15 hem. )
Consequence
MTMR1
NM_001306144.3 missense
NM_001306144.3 missense
Scores
1
6
10
Clinical Significance
Conservation
PhyloP100: 5.75
Genes affected
MTMR1 (HGNC:7449): (myotubularin related protein 1) This gene encodes a member of the myotubularin related family of proteins. Members of this family contain the consensus sequence for the active site of protein tyrosine phosphatases. Alternatively spliced variants have been described but their biological validity has not been determined. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.29573053).
BS2
High Hemizygotes in GnomAdExome4 at 15 gene
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000894 AC: 1AN: 111879Hom.: 0 Cov.: 23 AF XY: 0.0000294 AC XY: 1AN XY: 34063
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GnomAD3 exomes AF: 0.0000280 AC: 5AN: 178330Hom.: 0 AF XY: 0.0000159 AC XY: 1AN XY: 63028
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GnomAD4 exome AF: 0.0000541 AC: 59AN: 1091408Hom.: 0 Cov.: 29 AF XY: 0.0000419 AC XY: 15AN XY: 357584
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GnomAD4 genome AF: 0.00000894 AC: 1AN: 111879Hom.: 0 Cov.: 23 AF XY: 0.0000294 AC XY: 1AN XY: 34063
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 10, 2024 | The c.838G>T (p.A280S) alteration is located in exon 8 (coding exon 8) of the MTMR1 gene. This alteration results from a G to T substitution at nucleotide position 838, causing the alanine (A) at amino acid position 280 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Pathogenic
D;.;D
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;T;D
M_CAP
Benign
D
MetaRNN
Benign
T;T;T
MetaSVM
Uncertain
D
MutationAssessor
Benign
L;.;.
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N
REVEL
Uncertain
Sift
Benign
T;T;T
Sift4G
Benign
T;T;T
Polyphen
B;B;B
Vest4
MVP
ClinPred
T
GERP RS
Varity_R
gMVP
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