rs1046282
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001983.4(ERCC1):c.*2261T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 582,008 control chromosomes in the GnomAD database, including 22,094 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.30 ( 7209 hom., cov: 32)
Exomes 𝑓: 0.26 ( 14885 hom. )
Consequence
ERCC1
NM_001983.4 3_prime_UTR
NM_001983.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.96
Genes affected
ERCC1 (HGNC:3433): (ERCC excision repair 1, endonuclease non-catalytic subunit) The product of this gene functions in the nucleotide excision repair pathway, and is required for the repair of DNA lesions such as those induced by UV light or formed by electrophilic compounds including cisplatin. The encoded protein forms a heterodimer with the XPF endonuclease (also known as ERCC4), and the heterodimeric endonuclease catalyzes the 5' incision in the process of excising the DNA lesion. The heterodimeric endonuclease is also involved in recombinational DNA repair and in the repair of inter-strand crosslinks. Mutations in this gene result in cerebrooculofacioskeletal syndrome, and polymorphisms that alter expression of this gene may play a role in carcinogenesis. Multiple transcript variants encoding different isoforms have been found for this gene. The last exon of this gene overlaps with the CD3e molecule, epsilon associated protein gene on the opposite strand. [provided by RefSeq, Oct 2009]
POLR1G (HGNC:24219): (RNA polymerase I subunit G) Enables RNA binding activity. Predicted to be involved in transmembrane receptor protein tyrosine kinase signaling pathway. Predicted to act upstream of or within rRNA transcription. Located in cytosol; mitochondrion; and nuclear lumen. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ERCC1 | NM_001983.4 | c.*2261T>C | 3_prime_UTR_variant | 10/10 | ENST00000300853.8 | ||
POLR1G | NM_012099.3 | c.164+179A>G | intron_variant | ENST00000309424.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ERCC1 | ENST00000300853.8 | c.*2261T>C | 3_prime_UTR_variant | 10/10 | 1 | NM_001983.4 | P1 | ||
POLR1G | ENST00000309424.8 | c.164+179A>G | intron_variant | 1 | NM_012099.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.300 AC: 45652AN: 151986Hom.: 7189 Cov.: 32
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GnomAD4 exome AF: 0.257 AC: 110649AN: 429902Hom.: 14885 Cov.: 5 AF XY: 0.259 AC XY: 59151AN XY: 228166
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GnomAD4 genome ? AF: 0.301 AC: 45722AN: 152106Hom.: 7209 Cov.: 32 AF XY: 0.300 AC XY: 22338AN XY: 74370
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at