rs801193
Positions:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NR_111973.1(RABGEF1P1):n.509-4950A>G variant causes a intron, non coding transcript 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 0.0040 ( 0 hom., cov: 31)
Failed GnomAD Quality Control
Consequence
RABGEF1P1
NR_111973.1 intron, non_coding_transcript
NR_111973.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.20
Genes affected
RABGEF1P1 (HGNC:55751): (RABGEF1 pseudogene 1)
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RABGEF1P1 | NR_111973.1 | n.509-4950A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RABGEF1P1 | ENST00000428370.1 | n.329+7764A>G | intron_variant, non_coding_transcript_variant | |||||||
ENST00000692299.1 | n.307+7760A>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 562AN: 139376Hom.: 0 Cov.: 31 FAILED QC
GnomAD3 genomes
AF:
AC:
562
AN:
139376
Hom.:
Cov.:
31
FAILED QC
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
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: AS_VQSR AF: 0.00403 AC: 562AN: 139492Hom.: 0 Cov.: 31 AF XY: 0.00485 AC XY: 330AN XY: 68060
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
562
AN:
139492
Hom.:
Cov.:
31
AF XY:
AC XY:
330
AN XY:
68060
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
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