13-24527029-G-T

Variant names:

• chr13-24527029-G-T
• rs2862909
• ENST00000445572.5:n.234-54632G>T

Variant summary

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

The ENST00000445572.5(TPTE2P6):​n.234-54632G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.627 in 152,108 control chromosomes in the GnomAD database, including 29,922 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 0.63 (29922 hom., cov: 34)
• Consequence: TPTE2P6 ENST00000445572.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.481
• Publications: 5 publications found

Genes affected

TPTE2P6 (HGNC:42644): (TPTE2 pseudogene 6)

ENSG00000288103 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000445572.5. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TPTE2P6	ENST00000445572.5	TSL:6	n.234-54632G>T		intron	N/A
	ENSG00000288103	ENST00000668417.2		n.616-1816G>T		intron	N/A
	ENSG00000288103	ENST00000787147.1		n.501-1816G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.627 AC: 95254 AN: 151990 Hom.: 29895 Cov.: 34

Gnomad AFR AF: 0.653

Gnomad AMI AF: 0.449

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.564

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.612

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.627 AC: 95332 AN: 152108 Hom.: 29922 Cov.: 34 AF XY: 0.630 AC XY: 46824 AN XY: 74372

African (AFR) AF: 0.653 AC: 27106 AN: 41496

American (AMR) AF: 0.628 AC: 9595 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.564 AC: 1956 AN: 3468

East Asian (EAS) AF: 0.653 AC: 3385 AN: 5182

South Asian (SAS) AF: 0.645 AC: 3116 AN: 4830

European-Finnish (FIN) AF: 0.643 AC: 6797 AN: 10574

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.612 AC: 41579 AN: 67964

Other (OTH) AF: 0.592 AC: 1249 AN: 2110

Alfa AF: 0.620 Hom.: 13722

Bravo AF: 0.620

Asia WGS AF: 0.656 AC: 2281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.51
DANN	Benign	0.45
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs2862909; hg19: chr13-25101167;