rs5995572

Variant names:

• chr22-38357306-A-G
• rs5995572
• ENST00000400206.7:c.-112+4093T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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:):

TPTEP2 (HGNC:53828): (TPTE pseudogene 2)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001289912.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TPTEP2-CSNK1E	NM_001289912.2		c.-112+4093T>C		intron	N/A	NP_001276841.1
	TPTEP2	NR_002821.2		n.417+4093T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TPTEP2-CSNK1E	ENST00000400206.7	TSL:2	c.-112+4093T>C		intron	N/A	ENSP00000383067.2
	ENSG00000291015	ENST00000407491.6	TSL:3	n.364+4093T>C		intron	N/A
	ENSG00000291015	ENST00000428294.5	TSL:5	n.407+4093T>C		intron	N/A

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

African (AFR) AF: 0.387 AC: 15793 AN: 40780

American (AMR) AF: 0.168 AC: 2523 AN: 15030

Ashkenazi Jewish (ASJ) AF: 0.0375 AC: 129 AN: 3436

East Asian (EAS) AF: 0.189 AC: 970 AN: 5142

South Asian (SAS) AF: 0.0329 AC: 156 AN: 4748

European-Finnish (FIN) AF: 0.0133 AC: 135 AN: 10118

Middle Eastern (MID) AF: 0.0517 AC: 15 AN: 290

European-Non Finnish (NFE) AF: 0.0210 AC: 1413 AN: 67270

Other (OTH) AF: 0.127 AC: 263 AN: 2066

Alfa AF: 0.0633 Hom.: 2297

Bravo AF: 0.166

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.24
DANN	Benign	0.47
PhyloP100		-0.93
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs5995572; hg19: chr22-38753311;