chr8-98033655-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002380.5(MATN2):āc.2811G>Cā(p.Gln937His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000395 in 1,587,982 control chromosomes in the GnomAD database, including 1 homozygotes. 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 (ā ).
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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MATN2 | NM_002380.5 | c.2811G>C | p.Gln937His | missense_variant | 18/19 | ENST00000254898.7 | NP_002371.3 | |
MATN2 | NM_030583.4 | c.2754G>C | p.Gln918His | missense_variant | 18/19 | NP_085072.2 | ||
MATN2 | NM_001317748.2 | c.2688G>C | p.Gln896His | missense_variant | 17/18 | NP_001304677.1 | ||
MATN2 | XM_005250920.3 | c.2397G>C | p.Gln799His | missense_variant | 17/18 | XP_005250977.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MATN2 | ENST00000254898.7 | c.2811G>C | p.Gln937His | missense_variant | 18/19 | 1 | NM_002380.5 | ENSP00000254898.6 | ||
MATN2 | ENST00000520016.5 | c.2811G>C | p.Gln937His | missense_variant | 17/18 | 1 | ENSP00000430487.1 | |||
MATN2 | ENST00000521689.5 | c.2754G>C | p.Gln918His | missense_variant | 18/19 | 1 | ENSP00000429977.1 | |||
MATN2 | ENST00000524308.5 | c.2688G>C | p.Gln896His | missense_variant | 17/18 | 1 | ENSP00000430221.1 | |||
MATN2 | ENST00000518154.5 | c.2100G>C | p.Gln700His | missense_variant | 15/16 | 1 | ENSP00000429622.1 | |||
MATN2 | ENST00000522025.6 | c.1959G>C | p.Gln653His | missense_variant | 17/18 | 5 | ENSP00000429010.1 | |||
MATN2 | ENST00000521952.5 | n.*479G>C | non_coding_transcript_exon_variant | 8/9 | 5 | ENSP00000429256.1 | ||||
MATN2 | ENST00000521952.5 | n.*479G>C | 3_prime_UTR_variant | 8/9 | 5 | ENSP00000429256.1 |
Frequencies
GnomAD3 genomes AF: 0.000355 AC: 54AN: 152186Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000292 AC: 66AN: 225776Hom.: 0 AF XY: 0.000230 AC XY: 28AN XY: 121488
GnomAD4 exome AF: 0.000399 AC: 573AN: 1435678Hom.: 1 Cov.: 27 AF XY: 0.000401 AC XY: 286AN XY: 713490
GnomAD4 genome AF: 0.000355 AC: 54AN: 152304Hom.: 0 Cov.: 33 AF XY: 0.000389 AC XY: 29AN XY: 74478
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 06, 2024 | The c.2811G>C (p.Q937H) alteration is located in exon 18 (coding exon 17) of the MATN2 gene. This alteration results from a G to C substitution at nucleotide position 2811, causing the glutamine (Q) at amino acid position 937 to be replaced by a histidine (H). 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