rs7289981

Positions:

• chr22-38323957-C-T

Variant summary

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

The NM_001289912.2(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 NM_001289912.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.34

Genes affected

TPTEP2-CSNK1E (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
TPTEP2-CSNK1E	NM_001289912.2	c.-12-9788G>A		intron_variant			NP_001276841.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.303

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.00233

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.149

Alfa AF: 0.135 Hom.: 2385

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7289981; hg19: chr22-38719962;