11-62596735-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_004739.4(MTA2):c.784C>T(p.Arg262Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,840 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004739.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MTA2 | NM_004739.4 | c.784C>T | p.Arg262Trp | missense_variant | Exon 9 of 18 | ENST00000278823.7 | NP_004730.2 | |
MTA2 | NM_001330292.2 | c.265C>T | p.Arg89Trp | missense_variant | Exon 9 of 18 | NP_001317221.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MTA2 | ENST00000278823.7 | c.784C>T | p.Arg262Trp | missense_variant | Exon 9 of 18 | 1 | NM_004739.4 | ENSP00000278823.2 | ||
MTA2 | ENST00000524902.5 | c.265C>T | p.Arg89Trp | missense_variant | Exon 7 of 16 | 1 | ENSP00000431346.1 | |||
MTA2 | ENST00000527204.5 | c.265C>T | p.Arg89Trp | missense_variant | Exon 9 of 18 | 2 | ENSP00000431797.1 | |||
MTA2 | ENST00000531261.1 | n.*31C>T | downstream_gene_variant | 4 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461840Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 727220
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.784C>T (p.R262W) alteration is located in exon 9 (coding exon 9) of the MTA2 gene. This alteration results from a C to T substitution at nucleotide position 784, causing the arginine (R) at amino acid position 262 to be replaced by a tryptophan (W). 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
Publications
No publications associated with this variant yet.