19-45363958-T-TG
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_000400.4(ERCC2):c.949+27_949+28insC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 1,531,696 control chromosomes in the GnomAD database, including 55,811 homozygotes. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.36 ( 14555 hom., cov: 0)
Exomes 𝑓: 0.22 ( 41256 hom. )
Consequence
ERCC2
NM_000400.4 intron
NM_000400.4 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.0850
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 -16 ACMG points.
BP6
Variant 19-45363958-T-TG is Benign according to our data. Variant chr19-45363958-T-TG is described in ClinVar as [Benign]. Clinvar id is 256023.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.737 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ERCC2 | NM_000400.4 | c.949+27_949+28insC | intron_variant | ENST00000391945.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ERCC2 | ENST00000391945.10 | c.949+27_949+28insC | intron_variant | 1 | NM_000400.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.364 AC: 55284AN: 151798Hom.: 14516 Cov.: 0
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GnomAD3 exomes AF: 0.275 AC: 37160AN: 135026Hom.: 6497 AF XY: 0.264 AC XY: 19514AN XY: 73870
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GnomAD4 exome AF: 0.223 AC: 307955AN: 1379780Hom.: 41256 Cov.: 36 AF XY: 0.222 AC XY: 151308AN XY: 681302
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GnomAD4 genome AF: 0.365 AC: 55382AN: 151916Hom.: 14555 Cov.: 0 AF XY: 0.361 AC XY: 26786AN XY: 74256
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 11, 2018 | - - |
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at