11-62596656-T-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_004739.4(MTA2):āc.863A>Gā(p.Asn288Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000236 in 1,613,102 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
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.863A>G | p.Asn288Ser | missense_variant | Exon 9 of 18 | ENST00000278823.7 | NP_004730.2 | |
MTA2 | NM_001330292.2 | c.344A>G | p.Asn115Ser | 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.863A>G | p.Asn288Ser | missense_variant | Exon 9 of 18 | 1 | NM_004739.4 | ENSP00000278823.2 | ||
MTA2 | ENST00000524902.5 | c.344A>G | p.Asn115Ser | missense_variant | Exon 7 of 16 | 1 | ENSP00000431346.1 | |||
MTA2 | ENST00000527204.5 | c.344A>G | p.Asn115Ser | missense_variant | Exon 9 of 18 | 2 | ENSP00000431797.1 | |||
MTA2 | ENST00000531179.1 | n.6A>G | non_coding_transcript_exon_variant | Exon 1 of 3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152200Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000440 AC: 11AN: 250026Hom.: 0 AF XY: 0.0000370 AC XY: 5AN XY: 135160
GnomAD4 exome AF: 0.0000205 AC: 30AN: 1460784Hom.: 0 Cov.: 32 AF XY: 0.0000220 AC XY: 16AN XY: 726710
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152318Hom.: 0 Cov.: 32 AF XY: 0.0000671 AC XY: 5AN XY: 74494
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.863A>G (p.N288S) alteration is located in exon 9 (coding exon 9) of the MTA2 gene. This alteration results from a A to G substitution at nucleotide position 863, causing the asparagine (N) at amino acid position 288 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