ENST00000413269.3:n.460+27211C>A

Variant names:

• chr9-68569853-C-A
• rs7046236
• ENST00000413269.3:n.460+27211C>A

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The ENST00000413269.3(TMEM252-DT):​n.460+27211C>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: 33)
• Consequence: TMEM252-DT ENST00000413269.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190
• Publications: 7 publications found

Genes affected

TMEM252-DT (HGNC:54377): (TMEM252 divergent transcript)

LINC01506 (HGNC:51187): (long intergenic non-protein coding RNA 1506)

ENSG00000299330 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMEM252-DT	NR_187592.1	n.471+27211C>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM252-DT	ENST00000413269.3	n.460+27211C>A		intron_variant	Intron 2 of 4	1
LINC01506	ENST00000762443.1	n.356-24229G>T		intron_variant	Intron 2 of 2
LINC01506	ENST00000762444.1	n.88+14258G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	12
DANN	Benign	0.76
PhyloP100		0.019

Splicing

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

Other links and lift over

dbSNP: rs7046236; hg19: chr9-71184769;