18-58416822-T-A
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000585470.1(ENSG00000267675):n.58T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 34)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
ENSG00000267675
ENST00000585470.1 non_coding_transcript_exon
ENST00000585470.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.05
Publications
15 publications found
Genes affected
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| ENSG00000267675 | ENST00000585470.1 | n.58T>A | non_coding_transcript_exon_variant | Exon 1 of 2 | 5 | |||||
| ENSG00000300063 | ENST00000768485.1 | n.157+2310A>T | intron_variant | Intron 2 of 3 | ||||||
| ENSG00000300063 | ENST00000768488.1 | n.297+2310A>T | intron_variant | Intron 2 of 3 | ||||||
| ENSG00000300063 | ENST00000768489.1 | n.313+2310A>T | intron_variant | Intron 3 of 4 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
34
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 116Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 86
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
AC:
0
AN:
116
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
86
African (AFR)
AF:
AC:
0
AN:
4
American (AMR)
AF:
AC:
0
AN:
4
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
2
East Asian (EAS)
AF:
AC:
0
AN:
6
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AC:
0
AN:
0
Middle Eastern (MID)
AF:
AC:
0
AN:
2
European-Non Finnish (NFE)
AF:
AC:
0
AN:
92
Other (OTH)
AF:
AC:
0
AN:
6
GnomAD4 genome
GnomAD4 genome
Cov.:
34
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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