rs56170134
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The ENST00000391945.10(ERCC2):c.1119-25_1119-24insC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00293 in 1,547,836 control chromosomes in the GnomAD database, including 100 homozygotes. Variant has been reported in ClinVar as Benign (★). There are indicators that this mutation may affect the branch point..
Frequency
Genomes: 𝑓 0.014 ( 52 hom., cov: 31)
Exomes 𝑓: 0.0017 ( 48 hom. )
Consequence
ERCC2
ENST00000391945.10 intron
ENST00000391945.10 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.478
Genes affected
ERCC2 (HGNC:3434): (ERCC excision repair 2, TFIIH core complex helicase subunit) The nucleotide excision repair pathway is a mechanism to repair damage to DNA. The protein encoded by this gene is involved in transcription-coupled nucleotide excision repair and is an integral member of the basal transcription factor BTF2/TFIIH complex. The gene product has ATP-dependent DNA helicase activity and belongs to the RAD3/XPD subfamily of helicases. Defects in this gene can result in three different disorders, the cancer-prone syndrome xeroderma pigmentosum complementation group D, trichothiodystrophy, and Cockayne syndrome. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 19-45361666-C-CG is Benign according to our data. Variant chr19-45361666-C-CG is described in ClinVar as [Benign]. Clinvar id is 135525.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0501 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ERCC2 | NM_000400.4 | c.1119-25_1119-24insC | intron_variant | ENST00000391945.10 | NP_000391.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ERCC2 | ENST00000391945.10 | c.1119-25_1119-24insC | intron_variant | 1 | NM_000400.4 | ENSP00000375809 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0144 AC: 2191AN: 152034Hom.: 52 Cov.: 31
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GnomAD3 exomes AF: 0.00414 AC: 1034AN: 249876Hom.: 22 AF XY: 0.00310 AC XY: 419AN XY: 135216
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GnomAD4 exome AF: 0.00168 AC: 2346AN: 1395684Hom.: 48 Cov.: 22 AF XY: 0.00148 AC XY: 1033AN XY: 697814
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GnomAD4 genome AF: 0.0144 AC: 2192AN: 152152Hom.: 52 Cov.: 31 AF XY: 0.0138 AC XY: 1028AN XY: 74424
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ClinVar
Significance: Benign
Submissions summary: Benign:1Other:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 24, 2019 | - - |
not specified Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at