chr1-40304805-T-G
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 2P and 20B. PM1BP4_StrongBP6_Very_StrongBS1BS2
The NM_001852.4(COL9A2):āc.1150A>Cā(p.Met384Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00132 in 1,550,918 control chromosomes in the GnomAD database, including 22 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Uncertain significancein ClinVar.
Frequency
Consequence
NM_001852.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL9A2 | NM_001852.4 | c.1150A>C | p.Met384Leu | missense_variant | 22/32 | ENST00000372748.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL9A2 | ENST00000372748.8 | c.1150A>C | p.Met384Leu | missense_variant | 22/32 | 1 | NM_001852.4 | P1 | |
COL9A2 | ENST00000482722.5 | n.1453A>C | non_coding_transcript_exon_variant | 21/31 | 1 | ||||
COL9A2 | ENST00000466267.1 | n.115A>C | non_coding_transcript_exon_variant | 2/11 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00700 AC: 1065AN: 152172Hom.: 9 Cov.: 32
GnomAD3 exomes AF: 0.00174 AC: 271AN: 155948Hom.: 3 AF XY: 0.00122 AC XY: 100AN XY: 82044
GnomAD4 exome AF: 0.000699 AC: 977AN: 1398626Hom.: 13 Cov.: 31 AF XY: 0.000583 AC XY: 402AN XY: 689878
GnomAD4 genome AF: 0.00699 AC: 1064AN: 152292Hom.: 9 Cov.: 32 AF XY: 0.00673 AC XY: 501AN XY: 74460
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 30, 2019 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Connective tissue disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | May 01, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at