chr6-111307527-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PP2BP4_StrongBP6_ModerateBS2
The NM_001372078.1(REV3L):c.9086G>A(p.Arg3029Gln) variant causes a missense change. The variant allele was found at a frequency of 0.000122 in 1,614,164 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00026 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00011 ( 0 hom. )
Consequence
REV3L
NM_001372078.1 missense
NM_001372078.1 missense
Scores
4
13
Clinical Significance
Conservation
PhyloP100: 4.83
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 -9 ACMG points.
PP2
?
Missense variant where missense usually causes diseases, REV3L
BP4
?
Computational evidence support a benign effect (MetaRNN=0.008150727).
BP6
?
Variant 6-111307527-C-T is Benign according to our data. Variant chr6-111307527-C-T is described in ClinVar as [Benign]. Clinvar id is 720269.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAd at 40 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
REV3L | NM_001372078.1 | c.9086G>A | p.Arg3029Gln | missense_variant | 31/32 | ENST00000368802.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
REV3L | ENST00000368802.8 | c.9086G>A | p.Arg3029Gln | missense_variant | 31/32 | 1 | NM_001372078.1 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000263 AC: 40AN: 152162Hom.: 0 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.000414 AC: 104AN: 251424Hom.: 0 AF XY: 0.000361 AC XY: 49AN XY: 135888
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GnomAD4 exome AF: 0.000107 AC: 157AN: 1461884Hom.: 0 Cov.: 32 AF XY: 0.000106 AC XY: 77AN XY: 727240
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GnomAD4 genome ? AF: 0.000263 AC: 40AN: 152280Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74450
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Mar 29, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Uncertain
DEOGEN2
Benign
T;T;.;T
Eigen
Benign
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N;N
REVEL
Benign
Sift
Benign
T;T;T;T
Sift4G
Benign
T;T;T;T
Polyphen
P;P;.;P
Vest4
MVP
MPC
1.7
ClinPred
T
GERP RS
Varity_R
gMVP
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