chrX-112403236-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001395362.2(RTL4):c.-284-27878C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.63 ( 16608 hom., 20673 hem., cov: 22)
Failed GnomAD Quality Control
Consequence
RTL4
NM_001395362.2 intron
NM_001395362.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.343
Genes affected
RTL4 (HGNC:25214): (retrotransposon Gag like 4) Predicted to enable nucleic acid binding activity and zinc ion binding activity. Predicted to act upstream of or within cognition and norepinephrine metabolic process. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BS2
?
High Homozygotes in GnomAd at 16618 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RTL4 | NM_001395362.2 | c.-284-27878C>T | intron_variant | ENST00000695839.1 | |||
RTL4 | NM_001004308.3 | c.-229-51264C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RTL4 | ENST00000695839.1 | c.-284-27878C>T | intron_variant | NM_001395362.2 | P1 | ||||
RTL4 | ENST00000340433.4 | c.-284-27878C>T | intron_variant | P1 | |||||
RTL4 | ENST00000695808.1 | c.-229-51264C>T | intron_variant | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.633 AC: 69901AN: 110386Hom.: 16618 Cov.: 22 AF XY: 0.633 AC XY: 20655AN XY: 32646
GnomAD3 genomes
?
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69901
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110386
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22
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20655
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Data not reliable, filtered out with message: InbreedingCoeff AF: 0.633 AC: 69891AN: 110437Hom.: 16608 Cov.: 22 AF XY: 0.632 AC XY: 20673AN XY: 32705
GnomAD4 genome
?
Data not reliable, filtered out with message: InbreedingCoeff
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at