8-98027434-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_002380.5(MATN2):c.1961T>C(p.Ile654Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000186 in 1,453,888 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MATN2 | NM_002380.5 | c.1961T>C | p.Ile654Thr | missense_variant | Exon 14 of 19 | ENST00000254898.7 | NP_002371.3 | |
MATN2 | NM_030583.4 | c.1961T>C | p.Ile654Thr | missense_variant | Exon 14 of 19 | NP_085072.2 | ||
MATN2 | NM_001317748.2 | c.1838T>C | p.Ile613Thr | missense_variant | Exon 13 of 18 | NP_001304677.1 | ||
MATN2 | XM_005250920.3 | c.1943-3028T>C | intron_variant | Intron 13 of 17 | XP_005250977.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MATN2 | ENST00000254898.7 | c.1961T>C | p.Ile654Thr | missense_variant | Exon 14 of 19 | 1 | NM_002380.5 | ENSP00000254898.6 | ||
MATN2 | ENST00000520016.5 | c.1961T>C | p.Ile654Thr | missense_variant | Exon 13 of 18 | 1 | ENSP00000430487.1 | |||
MATN2 | ENST00000521689.5 | c.1961T>C | p.Ile654Thr | missense_variant | Exon 14 of 19 | 1 | ENSP00000429977.1 | |||
MATN2 | ENST00000524308.5 | c.1838T>C | p.Ile613Thr | missense_variant | Exon 13 of 18 | 1 | ENSP00000430221.1 | |||
MATN2 | ENST00000518154.5 | c.1307T>C | p.Ile436Thr | missense_variant | Exon 11 of 16 | 1 | ENSP00000429622.1 | |||
MATN2 | ENST00000522025.6 | c.1109T>C | p.Ile370Thr | missense_variant | Exon 13 of 18 | 5 | ENSP00000429010.1 | |||
MATN2 | ENST00000521952.5 | n.*25-3028T>C | intron_variant | Intron 4 of 8 | 5 | ENSP00000429256.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000242 AC: 6AN: 248248Hom.: 0 AF XY: 0.0000297 AC XY: 4AN XY: 134676
GnomAD4 exome AF: 0.0000186 AC: 27AN: 1453888Hom.: 0 Cov.: 31 AF XY: 0.0000222 AC XY: 16AN XY: 721454
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1961T>C (p.I654T) alteration is located in exon 14 (coding exon 13) of the MATN2 gene. This alteration results from a T to C substitution at nucleotide position 1961, causing the isoleucine (I) at amino acid position 654 to be replaced by a threonine (T). 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