chr11-47639023-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_014342.4(MTCH2):c.116T>C(p.Ile39Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000387 in 1,602,190 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014342.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MTCH2 | NM_014342.4 | c.116T>C | p.Ile39Thr | missense_variant | 2/13 | ENST00000302503.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MTCH2 | ENST00000302503.8 | c.116T>C | p.Ile39Thr | missense_variant | 2/13 | 1 | NM_014342.4 | P1 | |
MTCH2 | ENST00000530428.2 | c.116T>C | p.Ile39Thr | missense_variant | 2/12 | 5 | |||
MTCH2 | ENST00000533571.2 | n.163T>C | non_coding_transcript_exon_variant | 2/13 | 2 | ||||
MTCH2 | ENST00000539759.5 | n.103T>C | non_coding_transcript_exon_variant | 2/6 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000490 AC: 7AN: 142992Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000956 AC: 24AN: 251122Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135712
GnomAD4 exome AF: 0.0000377 AC: 55AN: 1459198Hom.: 0 Cov.: 32 AF XY: 0.0000289 AC XY: 21AN XY: 725766
GnomAD4 genome ? AF: 0.0000490 AC: 7AN: 142992Hom.: 0 Cov.: 33 AF XY: 0.0000721 AC XY: 5AN XY: 69354
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 16, 2021 | The c.116T>C (p.I39T) alteration is located in exon 2 (coding exon 2) of the MTCH2 gene. This alteration results from a T to C substitution at nucleotide position 116, causing the isoleucine (I) at amino acid position 39 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at