8-97978968-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002380.5(MATN2):c.1041T>A(p.His347Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,613,452 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 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.1041T>A | p.His347Gln | missense_variant | 6/19 | ENST00000254898.7 | |
MATN2 | NM_030583.4 | c.1041T>A | p.His347Gln | missense_variant | 6/19 | ||
MATN2 | NM_001317748.2 | c.1041T>A | p.His347Gln | missense_variant | 6/18 | ||
MATN2 | XM_005250920.3 | c.1041T>A | p.His347Gln | missense_variant | 6/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MATN2 | ENST00000254898.7 | c.1041T>A | p.His347Gln | missense_variant | 6/19 | 1 | NM_002380.5 | P4 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152202Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461250Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 726908
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152202Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74362
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 27, 2023 | The c.1041T>A (p.H347Q) alteration is located in exon 6 (coding exon 5) of the MATN2 gene. This alteration results from a T to A substitution at nucleotide position 1041, causing the histidine (H) at amino acid position 347 to be replaced by a glutamine (Q). 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