9-27610659-A-C
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000400348.3(CTAGE12P):n.87T>G 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
CTAGE12P
ENST00000400348.3 non_coding_transcript_exon
ENST00000400348.3 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.338
Publications
7 publications found
Genes affected
CTAGE12P (HGNC:37297): (CTAGE family member 12, pseudogene)
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=-0.95).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CTAGE12P | n.27610659A>C | intragenic_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CTAGE12P | ENST00000400348.3 | n.87T>G | non_coding_transcript_exon_variant | Exon 1 of 1 | 6 | |||||
ENSG00000307594 | ENST00000827310.1 | n.697-24273T>G | intron_variant | Intron 3 of 3 | ||||||
ENSG00000307594 | ENST00000827311.1 | n.389-24273T>G | intron_variant | Intron 1 of 1 |
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD3 genomes
Cov.:
34
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 382628Hom.: 0 Cov.: 2 AF XY: 0.00 AC XY: 0AN XY: 216666
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
382628
Hom.:
Cov.:
2
AF XY:
AC XY:
0
AN XY:
216666
African (AFR)
AF:
AC:
0
AN:
10336
American (AMR)
AF:
AC:
0
AN:
32502
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
11032
East Asian (EAS)
AF:
AC:
0
AN:
15462
South Asian (SAS)
AF:
AC:
0
AN:
62788
European-Finnish (FIN)
AF:
AC:
0
AN:
31138
Middle Eastern (MID)
AF:
AC:
0
AN:
2782
European-Non Finnish (NFE)
AF:
AC:
0
AN:
199028
Other (OTH)
AF:
AC:
0
AN:
17560
GnomAD4 genome Cov.: 34
GnomAD4 genome
Cov.:
34
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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