rs11615
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_001983(ERCC1):c.354T>C(p.Asn118=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.552 in 151840 control chromosomes in the gnomAD Genomes database, including 26919 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (β β ).
Frequency
Genomes: π 0.55 ( 26919 hom., cov: 31)
Exomes π: 0.50 ( 35330 hom. )
Consequence
ERCC1
NM_001983 synonymous
NM_001983 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.629
Links
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
Variant 19:45420395-A>G is Benign according to our data. Variant chr19-45420395-A-G is described in ClinVar as [Benign]. Clinvar id is 225945. Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-45420395-A-G is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=-0.629 with no splicing effect.
BA1
?
GnomAd highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.867 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ERCC1 | NM_001983.4 | c.354T>C | p.Asn118= | synonymous_variant | 4/10 | ENST00000300853.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ERCC1 | ENST00000300853.8 | c.354T>C | p.Asn118= | synonymous_variant | 4/10 | 1 | NM_001983.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.552 AC: 83875AN: 151840Hom.: 26919 Cov.: 31
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GnomAD3 exomes AF: 0.501 AC: 125107AN: 249686Hom.: 35330 AF XY: 0.485 AC XY: 65375AN XY: 134914
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 10, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 01, 2022 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at