chr8-98003762-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002380.5(MATN2):c.1306C>A(p.Pro436Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000106 in 1,613,746 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MATN2 | NM_002380.5 | c.1306C>A | p.Pro436Thr | missense_variant | 8/19 | ENST00000254898.7 | |
MATN2 | NM_030583.4 | c.1306C>A | p.Pro436Thr | missense_variant | 8/19 | ||
MATN2 | NM_001317748.2 | c.1183C>A | p.Pro395Thr | missense_variant | 7/18 | ||
MATN2 | XM_005250920.3 | c.1306C>A | p.Pro436Thr | missense_variant | 8/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MATN2 | ENST00000254898.7 | c.1306C>A | p.Pro436Thr | missense_variant | 8/19 | 1 | NM_002380.5 | P4 |
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152142Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000305 AC: 76AN: 249054Hom.: 0 AF XY: 0.000244 AC XY: 33AN XY: 135126
GnomAD4 exome AF: 0.000105 AC: 154AN: 1461604Hom.: 0 Cov.: 32 AF XY: 0.0000935 AC XY: 68AN XY: 727094
GnomAD4 genome AF: 0.000112 AC: 17AN: 152142Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74308
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 04, 2023 | The c.1306C>A (p.P436T) alteration is located in exon 8 (coding exon 7) of the MATN2 gene. This alteration results from a C to A substitution at nucleotide position 1306, causing the proline (P) at amino acid position 436 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