rs954215121
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_005236.3(ERCC4):c.1899C>G(p.Leu633=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000827 in 1,451,888 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. L633L) has been classified as Likely benign.
Frequency
Consequence
NM_005236.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ERCC4 | NM_005236.3 | c.1899C>G | p.Leu633= | synonymous_variant | 9/11 | ENST00000311895.8 | |
ERCC4 | XM_011522424.4 | c.2037C>G | p.Leu679= | synonymous_variant | 10/12 | ||
ERCC4 | XM_047433774.1 | c.1110C>G | p.Leu370= | synonymous_variant | 6/8 | ||
ERCC4 | XM_011522427.2 | c.549C>G | p.Leu183= | synonymous_variant | 4/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ERCC4 | ENST00000311895.8 | c.1899C>G | p.Leu633= | synonymous_variant | 9/11 | 1 | NM_005236.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 251056Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135774
GnomAD4 exome AF: 0.00000827 AC: 12AN: 1451888Hom.: 0 Cov.: 28 AF XY: 0.00000415 AC XY: 3AN XY: 723082
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Cockayne syndrome;C0268140:Xeroderma pigmentosum, group F;C3808988:Fanconi anemia complementation group Q Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Apr 24, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at