rs2862909

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr13-24527029-G-A
• chr13-24527029-G-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000668417.1(ENSG00000288103):​n.251-1816G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 34)
• Consequence: ENSG00000288103 ENST00000668417.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.481

Genes affected

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

ENSG00000288103 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370117	XR_941755.2	n.677-1816G>A		intron_variant	Intron 2 of 2
LOC105370117	XR_941756.2	n.430-1816G>A		intron_variant	Intron 2 of 2
LOC105370117	XR_941758.2	n.479-1816G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TPTE2P6	ENST00000445572.5	n.234-54632G>A		intron_variant	Intron 3 of 9	6
ENSG00000288103	ENST00000668417.1	n.251-1816G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes Cov.: 34

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

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	0.63
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2862909; hg19: chr13-25101167;