9-121370602-A-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000637541.1(ENSG00000227355):n.112A>T 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: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
ENSG00000227355
ENST00000637541.1 non_coding_transcript_exon
ENST00000637541.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.424
Publications
8 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=-0.87).
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| LOC102723324 | NR_187150.1 | n.88A>T | non_coding_transcript_exon_variant | Exon 1 of 3 | ||||
| LOC102723324 | NR_187151.1 | n.88A>T | non_coding_transcript_exon_variant | Exon 1 of 3 | ||||
| LOC102723324 | NR_187152.1 | n.88A>T | non_coding_transcript_exon_variant | Exon 1 of 3 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| ENSG00000227355 | ENST00000637541.1 | n.112A>T | non_coding_transcript_exon_variant | Exon 1 of 3 | 3 | |||||
| ENSG00000227355 | ENST00000685727.2 | n.159A>T | non_coding_transcript_exon_variant | Exon 1 of 4 | ||||||
| ENSG00000227355 | ENST00000688457.2 | n.89A>T | non_coding_transcript_exon_variant | Exon 1 of 4 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 36070Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 19186
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
36070
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
19186
African (AFR)
AF:
AC:
0
AN:
1664
American (AMR)
AF:
AC:
0
AN:
2352
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
1196
East Asian (EAS)
AF:
AC:
0
AN:
2642
South Asian (SAS)
AF:
AC:
0
AN:
3098
European-Finnish (FIN)
AF:
AC:
0
AN:
1484
Middle Eastern (MID)
AF:
AC:
0
AN:
158
European-Non Finnish (NFE)
AF:
AC:
0
AN:
21474
Other (OTH)
AF:
AC:
0
AN:
2002
GnomAD4 genome
GnomAD4 genome
Cov.:
33
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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