11-62593952-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004739.4(MTA2):c.1930G>T(p.Ala644Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,858 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_004739.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MTA2 | NM_004739.4 | c.1930G>T | p.Ala644Ser | missense_variant | Exon 18 of 18 | ENST00000278823.7 | NP_004730.2 | |
MTA2 | NM_001330292.2 | c.1411G>T | p.Ala471Ser | 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.1930G>T | p.Ala644Ser | missense_variant | Exon 18 of 18 | 1 | NM_004739.4 | ENSP00000278823.2 | ||
MTA2 | ENST00000524902.5 | c.1411G>T | p.Ala471Ser | missense_variant | Exon 16 of 16 | 1 | ENSP00000431346.1 | |||
MTA2 | ENST00000527204.5 | c.1411G>T | p.Ala471Ser | missense_variant | Exon 18 of 18 | 2 | ENSP00000431797.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251094Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135700
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461858Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727238
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1930G>T (p.A644S) alteration is located in exon 18 (coding exon 18) of the MTA2 gene. This alteration results from a G to T substitution at nucleotide position 1930, causing the alanine (A) at amino acid position 644 to be replaced by a serine (S). 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