rs7289981

Variant names:

• chr22-38323957-C-T
• rs7289981
• ENST00000400206.7:c.-12-9788G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000400206.7(TPTEP2-CSNK1E):​c.-12-9788G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 152,000 control chromosomes in the GnomAD database, including 2,949 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 0.18 (2949 hom., cov: 31)
• Consequence: TPTEP2-CSNK1E ENST00000400206.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.34
• Publications: 12 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TPTEP2-CSNK1E	NM_001289912.2	c.-12-9788G>A		intron_variant	Intron 5 of 14		NP_001276841.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TPTEP2-CSNK1E	ENST00000400206.7	c.-12-9788G>A		intron_variant	Intron 5 of 14	2		ENSP00000383067.2

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26606 AN: 151884 Hom.: 2940 Cov.: 31

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.00232

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.175 AC: 26653 AN: 152000 Hom.: 2949 Cov.: 31 AF XY: 0.177 AC XY: 13128 AN XY: 74304

African (AFR) AF: 0.303 AC: 12541 AN: 41444

American (AMR) AF: 0.156 AC: 2373 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 438 AN: 3468

East Asian (EAS) AF: 0.00233 AC: 12 AN: 5154

South Asian (SAS) AF: 0.182 AC: 876 AN: 4804

European-Finnish (FIN) AF: 0.133 AC: 1405 AN: 10598

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8466 AN: 67962

Other (OTH) AF: 0.149 AC: 314 AN: 2108

Alfa AF: 0.138 Hom.: 3845

Bravo AF: 0.182

Asia WGS AF: 0.0920 AC: 321 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.34
DANN	Benign	0.58
PhyloP100		-3.3
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: rs7289981; hg19: chr22-38719962;