dbSNP rs13054361: TPTEP2-CSNK1E:c.-111-113C>T (chr22-38336819-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -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

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0280

Publications

3 publications found

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]

TPTEP2-CSNK1E links:

ENSG00000291015 (HGNC:):

ENSG00000291015 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000400206.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TPTEP2-CSNK1E	NM_001289912.2		c.-111-113C>T		intron	N/A	NP_001276841.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
TPTEP2-CSNK1E	ENST00000400206.7	TSL:2	c.-111-113C>T	intron	N/A	ENSP00000383067.2
ENSG00000291015	ENST00000428294.5	TSL:5	n.505-113C>T	intron	N/A
ENSG00000291015	ENST00000428606.1	TSL:2	n.255-113C>T	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0988

AC:

15024

AN:

152046

Hom.:

1095

Cov.:

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:

AN:

Hom.:

AF XY:

0.0556

AC XY:

AN XY:

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

Other (OTH)

AC:

AN:

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.375

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0987

AC:

15023

AN:

152166

Hom.:

1093

Cov.:

AF XY:

0.104

AC XY:

7701

AN XY:

74400

show subpopulations

African (AFR)

AF:

0.0712

AC:

2956

AN:

41530

American (AMR)

AF:

0.101

AC:

1546

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.111

AC:

385

AN:

3468

East Asian (EAS)

AF:

0.409

AC:

2109

AN:

5154

South Asian (SAS)

AF:

0.232

AC:

1118

AN:

4820

European-Finnish (FIN)

AF:

0.0888

AC:

941

AN:

10600

Middle Eastern (MID)

AF:

0.0918

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0836

AC:

5683

AN:

68002

Other (OTH)

AF:

0.106

AC:

223

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

661

1321

1982

2642

3303

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

184

368

552

736

920

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0939

Hom.:

728

Bravo

AF:

0.0980

Asia WGS

AF:

0.322

AC:

1120

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

4.3

(source)

DANN

Benign

0.79

PhyloP100

0.028

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over