chr11-62593994-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_004739.4(MTA2):c.1888C>T(p.Arg630Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,613,208 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 Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MTA2 | NM_004739.4 | c.1888C>T | p.Arg630Cys | missense_variant | Exon 18 of 18 | ENST00000278823.7 | NP_004730.2 | |
MTA2 | NM_001330292.2 | c.1369C>T | p.Arg457Cys | missense_variant | Exon 18 of 18 | NP_001317221.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MTA2 | ENST00000278823.7 | c.1888C>T | p.Arg630Cys | missense_variant | Exon 18 of 18 | 1 | NM_004739.4 | ENSP00000278823.2 | ||
MTA2 | ENST00000524902.5 | c.1369C>T | p.Arg457Cys | missense_variant | Exon 16 of 16 | 1 | ENSP00000431346.1 | |||
MTA2 | ENST00000527204.5 | c.1369C>T | p.Arg457Cys | missense_variant | Exon 18 of 18 | 2 | ENSP00000431797.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152220Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000802 AC: 2AN: 249284Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134724
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1460988Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 726786
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152220Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1888C>T (p.R630C) alteration is located in exon 18 (coding exon 18) of the MTA2 gene. This alteration results from a C to T substitution at nucleotide position 1888, causing the arginine (R) at amino acid position 630 to be replaced by a cysteine (C). 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