chr11-47634724-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_014342.4(MTCH2):c.317C>T(p.Pro106Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000106 in 1,601,908 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MTCH2 | NM_014342.4 | c.317C>T | p.Pro106Leu | missense_variant | 5/13 | ENST00000302503.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MTCH2 | ENST00000302503.8 | c.317C>T | p.Pro106Leu | missense_variant | 5/13 | 1 | NM_014342.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000198 AC: 3AN: 151456Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000449 AC: 11AN: 244850Hom.: 0 AF XY: 0.0000453 AC XY: 6AN XY: 132394
GnomAD4 exome AF: 0.00000965 AC: 14AN: 1450358Hom.: 0 Cov.: 29 AF XY: 0.0000125 AC XY: 9AN XY: 721564
GnomAD4 genome ? AF: 0.0000198 AC: 3AN: 151550Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 73978
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 14, 2021 | The c.317C>T (p.P106L) alteration is located in exon 5 (coding exon 5) of the MTCH2 gene. This alteration results from a C to T substitution at nucleotide position 317, causing the proline (P) at amino acid position 106 to be replaced by a leucine (L). 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