rs1418761
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_130398.4(EXO1):c.2109+241G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.944 in 152,300 control chromosomes in the GnomAD database, including 68,085 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 0.94 ( 68085 hom., cov: 33)
Consequence
EXO1
NM_130398.4 intron
NM_130398.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.371
Genes affected
EXO1 (HGNC:3511): (exonuclease 1) This gene encodes a protein with 5' to 3' exonuclease activity as well as an RNase H activity. It is similar to the Saccharomyces cerevisiae protein Exo1 which interacts with Msh2 and which is involved in mismatch repair and recombination. Alternative splicing of this gene results in three transcript variants encoding two different isoforms. [provided by RefSeq, Jul 2008]
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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=-0.86).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.97 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EXO1 | NM_130398.4 | c.2109+241G>A | intron_variant | ENST00000366548.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EXO1 | ENST00000366548.8 | c.2109+241G>A | intron_variant | 1 | NM_130398.4 | P2 | |||
EXO1 | ENST00000348581.9 | c.2109+241G>A | intron_variant | 1 | P2 | ||||
EXO1 | ENST00000518483.5 | c.2109+241G>A | intron_variant | 1 | A2 | ||||
EXO1 | ENST00000521202.2 | c.304+241G>A | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.944 AC: 143733AN: 152182Hom.: 68051 Cov.: 33
GnomAD3 genomes
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.944 AC: 143821AN: 152300Hom.: 68085 Cov.: 33 AF XY: 0.943 AC XY: 70248AN XY: 74456
GnomAD4 genome
?
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33
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70248
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74456
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3186
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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