chr21-45488441-T-G
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_001379500.1(COL18A1):āc.1920T>Gā(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 (ā ). 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