chr11-62595840-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_004739.4(MTA2):c.1166G>A(p.Arg389His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000929 in 1,614,158 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004739.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MTA2 | NM_004739.4 | c.1166G>A | p.Arg389His | missense_variant | Exon 13 of 18 | ENST00000278823.7 | NP_004730.2 | |
MTA2 | NM_001330292.2 | c.647G>A | p.Arg216His | missense_variant | Exon 13 of 18 | NP_001317221.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MTA2 | ENST00000278823.7 | c.1166G>A | p.Arg389His | missense_variant | Exon 13 of 18 | 1 | NM_004739.4 | ENSP00000278823.2 | ||
MTA2 | ENST00000524902.5 | c.647G>A | p.Arg216His | missense_variant | Exon 11 of 16 | 1 | ENSP00000431346.1 | |||
MTA2 | ENST00000527204.5 | c.647G>A | p.Arg216His | missense_variant | Exon 13 of 18 | 2 | ENSP00000431797.1 | |||
MTA2 | ENST00000531179.1 | n.533G>A | non_coding_transcript_exon_variant | Exon 3 of 3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251468Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135908
GnomAD4 exome AF: 0.00000889 AC: 13AN: 1461886Hom.: 0 Cov.: 32 AF XY: 0.00000825 AC XY: 6AN XY: 727244
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152272Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74438
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1166G>A (p.R389H) alteration is located in exon 13 (coding exon 13) of the MTA2 gene. This alteration results from a G to A substitution at nucleotide position 1166, causing the arginine (R) at amino acid position 389 to be replaced by a histidine (H). 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