chr21-45510078-G-A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7
The NM_001379500.1(COL18A1):c.3510G>A(p.Ala1170=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000793 in 1,576,468 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. A1170A) has been classified as Likely benign.
Frequency
Consequence
NM_001379500.1 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL18A1 | NM_001379500.1 | c.3510G>A | p.Ala1170= | synonymous_variant | 40/42 | ENST00000651438.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL18A1 | ENST00000651438.1 | c.3510G>A | p.Ala1170= | synonymous_variant | 40/42 | NM_001379500.1 |
Frequencies
GnomAD3 genomes ? AF: 0.000591 AC: 90AN: 152198Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000523 AC: 96AN: 183634Hom.: 0 AF XY: 0.000560 AC XY: 57AN XY: 101726
GnomAD4 exome AF: 0.000815 AC: 1160AN: 1424152Hom.: 1 Cov.: 32 AF XY: 0.000753 AC XY: 532AN XY: 706328
GnomAD4 genome ? AF: 0.000591 AC: 90AN: 152316Hom.: 0 Cov.: 34 AF XY: 0.000604 AC XY: 45AN XY: 74474
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Mar 09, 2017 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 19, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at