rs465646
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1
The NM_001372078.1(REV3L):c.*461C>T variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.806 in 152,736 control chromosomes in the GnomAD database, including 49,778 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 0.81 ( 49604 hom., cov: 34)
Exomes 𝑓: 0.81 ( 174 hom. )
Consequence
REV3L
NM_001372078.1 3_prime_UTR
NM_001372078.1 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.43
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 -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.33).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
REV3L | NM_001372078.1 | c.*461C>T | 3_prime_UTR_variant | 32/32 | ENST00000368802.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
REV3L | ENST00000368802.8 | c.*461C>T | 3_prime_UTR_variant | 32/32 | 1 | NM_001372078.1 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.806 AC: 122554AN: 152084Hom.: 49570 Cov.: 34
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GnomAD4 exome AF: 0.807 AC: 431AN: 534Hom.: 174 Cov.: 0 AF XY: 0.805 AC XY: 248AN XY: 308
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GnomAD4 genome ? AF: 0.806 AC: 122646AN: 152202Hom.: 49604 Cov.: 34 AF XY: 0.803 AC XY: 59787AN XY: 74410
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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