9-68569853-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000413269.3(TMEM252-DT):​n.460+27211C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.607 in 152,058 control chromosomes in the GnomAD database, including 30,703 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 0.61 (30703 hom., 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: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.25).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.749 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMEM252-DT	NR_187592.1	n.471+27211C>T		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>T		intron_variant	Intron 2 of 4	1
LINC01506	ENST00000762443.1	n.356-24229G>A		intron_variant	Intron 2 of 2
LINC01506	ENST00000762444.1	n.88+14258G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.608 AC: 92305 AN: 151940 Hom.: 30688 Cov.: 33

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.784

Gnomad AMR AF: 0.716

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.769

Gnomad SAS AF: 0.756

Gnomad FIN AF: 0.715

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.716

Gnomad OTH AF: 0.634

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

GnomAD4 genome AF: 0.607 AC: 92349 AN: 152058 Hom.: 30703 Cov.: 33 AF XY: 0.612 AC XY: 45487 AN XY: 74314

African (AFR) AF: 0.312 AC: 12937 AN: 41458

American (AMR) AF: 0.716 AC: 10940 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.673 AC: 2337 AN: 3470

East Asian (EAS) AF: 0.769 AC: 3978 AN: 5170

South Asian (SAS) AF: 0.756 AC: 3646 AN: 4824

European-Finnish (FIN) AF: 0.715 AC: 7542 AN: 10552

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.716 AC: 48712 AN: 67988

Other (OTH) AF: 0.637 AC: 1346 AN: 2114

Alfa AF: 0.686 Hom.: 140200

Bravo AF: 0.593

Asia WGS AF: 0.744 AC: 2589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.25
CADD	Benign	12
DANN	Benign	0.73
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;