1-30718808-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002379.3(MATN1):c.591C>A(p.Asp197Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000963 in 1,610,364 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 (★).
Frequency
Consequence
NM_002379.3 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 |
---|---|---|---|---|---|---|---|
MATN1 | NM_002379.3 | c.591C>A | p.Asp197Glu | missense_variant | 3/8 | ENST00000373765.5 | |
MATN1-AS1 | NR_034182.1 | n.37G>T | non_coding_transcript_exon_variant | 1/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MATN1 | ENST00000373765.5 | c.591C>A | p.Asp197Glu | missense_variant | 3/8 | 1 | NM_002379.3 | P1 | |
MATN1-AS1 | ENST00000414532.6 | n.305G>T | non_coding_transcript_exon_variant | 1/4 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000724 AC: 11AN: 151960Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000162 AC: 40AN: 246578Hom.: 0 AF XY: 0.000157 AC XY: 21AN XY: 134128
GnomAD4 exome AF: 0.0000987 AC: 144AN: 1458404Hom.: 0 Cov.: 32 AF XY: 0.0000896 AC XY: 65AN XY: 725286
GnomAD4 genome ? AF: 0.0000724 AC: 11AN: 151960Hom.: 0 Cov.: 31 AF XY: 0.0000943 AC XY: 7AN XY: 74220
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 13, 2023 | The c.591C>A (p.D197E) alteration is located in exon 3 (coding exon 3) of the MATN1 gene. This alteration results from a C to A substitution at nucleotide position 591, causing the aspartic acid (D) at amino acid position 197 to be replaced by a glutamic acid (E). 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