5-139322772-T-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6BP7
The NM_018834.6(MATR3):āc.1953T>Gā(p.Leu651Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,864 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_018834.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MATR3 | NM_018834.6 | c.1953T>G | p.Leu651Leu | synonymous_variant | Exon 12 of 15 | ENST00000394805.8 | NP_061322.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MATR3 | ENST00000394805.8 | c.1953T>G | p.Leu651Leu | synonymous_variant | Exon 12 of 15 | 1 | NM_018834.6 | ENSP00000378284.3 | ||
MATR3 | ENST00000394800.6 | c.1953T>G | p.Leu651Leu | synonymous_variant | Exon 16 of 19 | 5 | ENSP00000378279.2 | |||
MATR3 | ENST00000502929.5 | c.1953T>G | p.Leu651Leu | synonymous_variant | Exon 17 of 20 | 2 | ENSP00000422319.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461864Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 727230
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
MATR3-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at