rs17511504
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The ENST00000368802.8(REV3L):c.9042+529C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0219 in 152,386 control chromosomes in the GnomAD database, including 53 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 0.022 ( 53 hom., cov: 31)
Exomes 𝑓: 0.027 ( 0 hom. )
Consequence
REV3L
ENST00000368802.8 intron
ENST00000368802.8 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.252
Genes affected
REV3L (HGNC:9968): (REV3 like, DNA directed polymerase zeta catalytic subunit) The protein encoded by this gene represents the catalytic subunit of DNA polymerase zeta, which functions in translesion DNA synthesis. The encoded protein can be found in mitochondria, where it protects DNA from damage. Defects in this gene are a cause of Mobius syndrome. [provided by RefSeq, Jan 2017]
MFSD4B (HGNC:21053): (major facilitator superfamily domain containing 4B) Predicted to enable glucose transmembrane transporter activity. Predicted to be involved in glucose transmembrane transport and sodium ion transport. Predicted to be located in apical plasma membrane. Predicted to be integral component of membrane. [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=-0.81).
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0219 (3333/152086) while in subpopulation NFE AF= 0.0324 (2203/67958). AF 95% confidence interval is 0.0313. There are 53 homozygotes in gnomad4. There are 1596 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
High AC in GnomAd4 at 3333 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
REV3L | NM_001372078.1 | c.9042+529C>T | intron_variant | ENST00000368802.8 | NP_001359007.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
REV3L | ENST00000368802.8 | c.9042+529C>T | intron_variant | 1 | NM_001372078.1 | ENSP00000357792 | P4 | |||
ENST00000607434.1 | n.122G>A | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes AF: 0.0219 AC: 3334AN: 151968Hom.: 53 Cov.: 31
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GnomAD4 exome AF: 0.0267 AC: 8AN: 300Hom.: 0 Cov.: 0 AF XY: 0.0194 AC XY: 4AN XY: 206
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GnomAD4 genome AF: 0.0219 AC: 3333AN: 152086Hom.: 53 Cov.: 31 AF XY: 0.0215 AC XY: 1596AN XY: 74358
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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