21-45488441-T-G
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_001379500.1(COL18A1):c.1920T>G(p.Leu640=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000411 in 1,461,574 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. L640L) has been classified as Benign.
Frequency
Consequence
NM_001379500.1 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL18A1 | NM_001379500.1 | c.1920T>G | p.Leu640= | synonymous_variant | 18/42 | ENST00000651438.1 | |
COL18A1 | NM_130444.3 | c.3165T>G | p.Leu1055= | synonymous_variant | 17/41 | ||
COL18A1 | NM_030582.4 | c.2460T>G | p.Leu820= | synonymous_variant | 17/41 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL18A1 | ENST00000651438.1 | c.1920T>G | p.Leu640= | synonymous_variant | 18/42 | NM_001379500.1 | |||
COL18A1 | ENST00000355480.10 | c.2460T>G | p.Leu820= | synonymous_variant | 17/41 | 1 | |||
COL18A1 | ENST00000359759.8 | c.3165T>G | p.Leu1055= | synonymous_variant | 17/41 | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 0AN: 151996Hom.: 0 Cov.: 32 FAILED QC
GnomAD3 exomes AF: 0.00000803 AC: 2AN: 249126Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135240
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1461574Hom.: 1 Cov.: 49 AF XY: 0.00000413 AC XY: 3AN XY: 727064
GnomAD4 genome ? Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 151996Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74230
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Feb 25, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at