rs1633091
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The ENST00000510438.1(MICE):n.471A>T variant causes a non coding transcript exon 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 0.0 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
MICE
ENST00000510438.1 non_coding_transcript_exon
ENST00000510438.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.231
Genes affected
MICE (HGNC:7094): (MHC class I polypeptide-related sequence E (pseudogene))
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=-0.89).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HLA-F-AS1 | NR_026973.1 | n.150+3811A>T | intron_variant, non_coding_transcript_variant | ||||
HLA-F-AS1 | NR_026972.1 | n.428+2059A>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MICE | ENST00000510438.1 | n.471A>T | non_coding_transcript_exon_variant | 3/6 | |||||
HLA-F-AS1 | ENST00000458236.1 | n.349+384A>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 0AN: 152084Hom.: 0 Cov.: 33 FAILED QC
GnomAD3 genomes
?
AF:
AC:
0
AN:
152084
Hom.:
Cov.:
33
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:
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 214712Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 124784
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
214712
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
124784
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 152084Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74286
GnomAD4 genome
?
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
152084
Hom.:
Cov.:
33
AF XY:
AC XY:
0
AN XY:
74286
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
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