rs778548131
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_004739.4(MTA2):c.1939C>T(p.Pro647Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000242 in 1,614,090 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_004739.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MTA2 | NM_004739.4 | c.1939C>T | p.Pro647Ser | missense_variant | Exon 18 of 18 | ENST00000278823.7 | NP_004730.2 | |
MTA2 | NM_001330292.2 | c.1420C>T | p.Pro474Ser | 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.1939C>T | p.Pro647Ser | missense_variant | Exon 18 of 18 | 1 | NM_004739.4 | ENSP00000278823.2 | ||
MTA2 | ENST00000524902.5 | c.1420C>T | p.Pro474Ser | missense_variant | Exon 16 of 16 | 1 | ENSP00000431346.1 | |||
MTA2 | ENST00000527204.5 | c.1420C>T | p.Pro474Ser | missense_variant | Exon 18 of 18 | 2 | ENSP00000431797.1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152216Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 250984Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135648
GnomAD4 exome AF: 0.0000239 AC: 35AN: 1461874Hom.: 0 Cov.: 31 AF XY: 0.0000303 AC XY: 22AN XY: 727240
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152216Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74352
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at