8-98030578-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002380.5(MATN2):c.2473G>A(p.Glu825Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000116 in 1,613,822 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 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MATN2 | NM_002380.5 | c.2473G>A | p.Glu825Lys | missense_variant | 15/19 | ENST00000254898.7 | |
MATN2 | NM_030583.4 | c.2473G>A | p.Glu825Lys | missense_variant | 15/19 | ||
MATN2 | NM_001317748.2 | c.2350G>A | p.Glu784Lys | missense_variant | 14/18 | ||
MATN2 | XM_005250920.3 | c.2059G>A | p.Glu687Lys | missense_variant | 14/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MATN2 | ENST00000254898.7 | c.2473G>A | p.Glu825Lys | missense_variant | 15/19 | 1 | NM_002380.5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000442 AC: 11AN: 248902Hom.: 0 AF XY: 0.0000370 AC XY: 5AN XY: 135020
GnomAD4 exome AF: 0.000123 AC: 180AN: 1461656Hom.: 0 Cov.: 31 AF XY: 0.000118 AC XY: 86AN XY: 727106
GnomAD4 genome ? AF: 0.0000526 AC: 8AN: 152166Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74330
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 02, 2022 | The c.2473G>A (p.E825K) alteration is located in exon 15 (coding exon 14) of the MATN2 gene. This alteration results from a G to A substitution at nucleotide position 2473, causing the glutamic acid (E) at amino acid position 825 to be replaced by a lysine (K). 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