rs5995572

Positions:

• chr22-38357306-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001289912.2(TPTEP2-CSNK1E):​c.-112+4093T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 149,784 control chromosomes in the GnomAD database, including 3,441 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 0.14 (3441 hom., cov: 32)
• Consequence: TPTEP2-CSNK1E NM_001289912.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.930

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]

ENSG00000291015 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TPTEP2-CSNK1E	NM_001289912.2	c.-112+4093T>C		intron_variant			NP_001276841.1
TPTEP2	NR_002821.2	n.417+4093T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TPTEP2-CSNK1E	ENST00000400206.7	c.-112+4093T>C		intron_variant		2		ENSP00000383067.2

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21338 AN: 149676 Hom.: 3427 Cov.: 32

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.00111

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.0375

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.0332

Gnomad FIN AF: 0.0133

Gnomad MID AF: 0.0577

Gnomad NFE AF: 0.0210

Gnomad OTH AF: 0.120

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.143 AC: 21398 AN: 149784 Hom.: 3441 Cov.: 32 AF XY: 0.141 AC XY: 10298 AN XY: 73114

Gnomad4 AFR AF: 0.387

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.0375

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.0329

Gnomad4 FIN AF: 0.0133

Gnomad4 NFE AF: 0.0210

Gnomad4 OTH AF: 0.127

Alfa AF: 0.0353 Hom.: 385

Bravo AF: 0.166

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.24
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5995572; hg19: chr22-38753311;