rs13054361

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000400206.7(TPTEP2-CSNK1E):​c.-111-113C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0987 in 152,186 control chromosomes in the GnomAD database, including 1,093 homozygotes. 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 0.099 ( 1093 hom., cov: 31)
Exomes 𝑓: 0.050 ( 0 hom. )

Consequence

TPTEP2-CSNK1E
ENST00000400206.7 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0280
Variant links:
Genes affected
TPTEP2-CSNK1E (HGNC:53829): (TPTEP2-CSNK1E readthrough) This locus represents naturally occurring readthrough transcription between the neighboring LOC400927 (transmembrane phosphoinositide 3-phosphatase and tensin homolog 2 pseudogene) and CSNK1E (casein kinase I isoform epsilon) genes on chromosome 22. The readthrough transcript encodes the same protein as the downstream gene product (casein kinase I isoform epsilon). [provided by RefSeq, Feb 2014]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TPTEP2-CSNK1ENM_001289912.2 linkuse as main transcriptc.-111-113C>T intron_variant NP_001276841.1 P49674Q5U045B3KRV2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TPTEP2-CSNK1EENST00000400206.7 linkuse as main transcriptc.-111-113C>T intron_variant 2 ENSP00000383067.2
ENSG00000291015ENST00000428294.5 linkuse as main transcriptn.505-113C>T intron_variant 5
ENSG00000291015ENST00000428606.1 linkuse as main transcriptn.255-113C>T intron_variant 2

Frequencies

GnomAD3 genomes
AF:
0.0988
AC:
15024
AN:
152046
Hom.:
1095
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0712
Gnomad AMI
AF:
0.0384
Gnomad AMR
AF:
0.101
Gnomad ASJ
AF:
0.111
Gnomad EAS
AF:
0.409
Gnomad SAS
AF:
0.232
Gnomad FIN
AF:
0.0888
Gnomad MID
AF:
0.0955
Gnomad NFE
AF:
0.0836
Gnomad OTH
AF:
0.107
GnomAD4 exome
AF:
0.0500
AC:
1
AN:
20
Hom.:
0
AF XY:
0.0556
AC XY:
1
AN XY:
18
show subpopulations
Gnomad4 AFR exome
AF:
0.500
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
GnomAD4 genome
AF:
0.0987
AC:
15023
AN:
152166
Hom.:
1093
Cov.:
31
AF XY:
0.104
AC XY:
7701
AN XY:
74400
show subpopulations
Gnomad4 AFR
AF:
0.0712
Gnomad4 AMR
AF:
0.101
Gnomad4 ASJ
AF:
0.111
Gnomad4 EAS
AF:
0.409
Gnomad4 SAS
AF:
0.232
Gnomad4 FIN
AF:
0.0888
Gnomad4 NFE
AF:
0.0836
Gnomad4 OTH
AF:
0.106
Alfa
AF:
0.0953
Hom.:
653
Bravo
AF:
0.0980
Asia WGS
AF:
0.322
AC:
1120
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
4.3
DANN
Benign
0.79

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs13054361; hg19: chr22-38732824; API