9-27610659-A-C

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.338

Publications

7 publications found
Variant links:
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
CTAGE12PENST00000400348.3 linkn.87T>G non_coding_transcript_exon_variant Exon 1 of 1 6
ENSG00000307594ENST00000827310.1 linkn.697-24273T>G intron_variant Intron 3 of 3
ENSG00000307594ENST00000827311.1 linkn.389-24273T>G intron_variant Intron 1 of 1

Frequencies

GnomAD3 genomes
Cov.:
34
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
382628
Hom.:
0
Cov.:
2
AF XY:
0.00
AC XY:
0
AN XY:
216666
African (AFR)
AF:
0.00
AC:
0
AN:
10336
American (AMR)
AF:
0.00
AC:
0
AN:
32502
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
11032
East Asian (EAS)
AF:
0.00
AC:
0
AN:
15462
South Asian (SAS)
AF:
0.00
AC:
0
AN:
62788
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
31138
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
2782
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
199028
Other (OTH)
AF:
0.00
AC:
0
AN:
17560
GnomAD4 genome
Cov.:
34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
3.1
DANN
Benign
0.38
PhyloP100
0.34

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs2889829; hg19: chr9-27610657; API