rs589362
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000288985.13(ERCC6L2):c.*186C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 401,512 control chromosomes in the GnomAD database, including 18,343 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 0.27 ( 5970 hom., cov: 32)
Exomes 𝑓: 0.31 ( 12373 hom. )
Consequence
ERCC6L2
ENST00000288985.13 3_prime_UTR
ENST00000288985.13 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.944
Genes affected
ERCC6L2 (HGNC:26922): (ERCC excision repair 6 like 2) This gene encodes a member of the Snf2 family of helicase-like proteins. The encoded protein may play a role in DNA repair and mitochondrial function. Mutations in this gene have been associated with bone marrow failure syndrome 2. Alternatively spliced transcript variants that encode different protein isoforms have been described. [provided by RefSeq, Apr 2014]
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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=-0.87).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ERCC6L2 | NM_020207.7 | c.2100+192C>G | intron_variant | ENST00000653738.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ERCC6L2 | ENST00000653738.2 | c.2100+192C>G | intron_variant | NM_020207.7 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.268 AC: 40714AN: 151894Hom.: 5972 Cov.: 32
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GnomAD4 exome AF: 0.310 AC: 77413AN: 249500Hom.: 12373 Cov.: 4 AF XY: 0.311 AC XY: 39732AN XY: 127726
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GnomAD4 genome ? AF: 0.268 AC: 40720AN: 152012Hom.: 5970 Cov.: 32 AF XY: 0.271 AC XY: 20099AN XY: 74284
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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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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at