22-38323184-A-G

Variant names:

• chr22-38323184-A-G
• rs5757037
• ENST00000400206.7:c.-12-9015T>C

Variant summary

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

The ENST00000400206.7(TPTEP2-CSNK1E):​c.-12-9015T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.638 in 152,050 control chromosomes in the GnomAD database, including 31,126 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 0.64 (31126 hom., cov: 32)
• Consequence: TPTEP2-CSNK1E ENST00000400206.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.222
• Publications: 14 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.669 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.-12-9015T>C		intron	N/A	NP_001276841.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TPTEP2-CSNK1E	ENST00000400206.7	TSL:2	c.-12-9015T>C		intron	N/A	ENSP00000383067.2

Frequencies

GnomAD3 genomes AF: 0.638 AC: 96917 AN: 151932 Hom.: 31085 Cov.: 32

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.709

Gnomad AMR AF: 0.680

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.479

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.638 AC: 97010 AN: 152050 Hom.: 31126 Cov.: 32 AF XY: 0.640 AC XY: 47551 AN XY: 74320

African (AFR) AF: 0.673 AC: 27891 AN: 41472

American (AMR) AF: 0.680 AC: 10399 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.505 AC: 1748 AN: 3464

East Asian (EAS) AF: 0.580 AC: 2988 AN: 5152

South Asian (SAS) AF: 0.479 AC: 2307 AN: 4816

European-Finnish (FIN) AF: 0.696 AC: 7361 AN: 10576

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.622 AC: 42277 AN: 67972

Other (OTH) AF: 0.597 AC: 1261 AN: 2112

Alfa AF: 0.621 Hom.: 64979

Bravo AF: 0.642

Asia WGS AF: 0.519 AC: 1807 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.85
DANN	Benign	0.64
PhyloP100		0.22
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: rs5757037; hg19: chr22-38719189;