8-98030470-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002380.5(MATN2):c.2365A>G(p.Met789Val) variant causes a missense change. The variant allele was found at a frequency of 0.00000372 in 1,613,142 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_002380.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MATN2 | NM_002380.5 | c.2365A>G | p.Met789Val | missense_variant | Exon 15 of 19 | ENST00000254898.7 | NP_002371.3 | |
MATN2 | NM_030583.4 | c.2365A>G | p.Met789Val | missense_variant | Exon 15 of 19 | NP_085072.2 | ||
MATN2 | NM_001317748.2 | c.2242A>G | p.Met748Val | missense_variant | Exon 14 of 18 | NP_001304677.1 | ||
MATN2 | XM_005250920.3 | c.1951A>G | p.Met651Val | missense_variant | Exon 14 of 18 | XP_005250977.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MATN2 | ENST00000254898.7 | c.2365A>G | p.Met789Val | missense_variant | Exon 15 of 19 | 1 | NM_002380.5 | ENSP00000254898.6 | ||
MATN2 | ENST00000520016.5 | c.2365A>G | p.Met789Val | missense_variant | Exon 14 of 18 | 1 | ENSP00000430487.1 | |||
MATN2 | ENST00000521689.5 | c.2365A>G | p.Met789Val | missense_variant | Exon 15 of 19 | 1 | ENSP00000429977.1 | |||
MATN2 | ENST00000524308.5 | c.2242A>G | p.Met748Val | missense_variant | Exon 14 of 18 | 1 | ENSP00000430221.1 | |||
MATN2 | ENST00000518154.5 | c.1711A>G | p.Met571Val | missense_variant | Exon 12 of 16 | 1 | ENSP00000429622.1 | |||
MATN2 | ENST00000522025.6 | c.1513A>G | p.Met505Val | missense_variant | Exon 14 of 18 | 5 | ENSP00000429010.1 | |||
MATN2 | ENST00000521952.5 | n.*33A>G | non_coding_transcript_exon_variant | Exon 5 of 9 | 5 | ENSP00000429256.1 | ||||
MATN2 | ENST00000521952.5 | n.*33A>G | 3_prime_UTR_variant | Exon 5 of 9 | 5 | ENSP00000429256.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152162Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000807 AC: 2AN: 247922Hom.: 0 AF XY: 0.00000743 AC XY: 1AN XY: 134526
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1460980Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 2AN XY: 726734
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152162Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2365A>G (p.M789V) alteration is located in exon 15 (coding exon 14) of the MATN2 gene. This alteration results from a A to G substitution at nucleotide position 2365, causing the methionine (M) at amino acid position 789 to be replaced by a valine (V). 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