rs7036795

Variant names:

• chr9-68553402-T-C
• rs7036795
• ENST00000413269.3:n.460+10760T>C

Variant summary

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

The ENST00000413269.3(TMEM252-DT):​n.460+10760T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 152,042 control chromosomes in the GnomAD database, including 2,873 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 0.19 (2873 hom., cov: 31)
• Consequence: TMEM252-DT ENST00000413269.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980
• Publications: 1 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMEM252-DT	NR_187592.1	n.471+10760T>C		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+10760T>C		intron_variant	Intron 2 of 4	1
LINC01506	ENST00000762443.1	n.356-7778A>G		intron_variant	Intron 2 of 2
LINC01506	ENST00000762444.1	n.89-7778A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29105 AN: 151924 Hom.: 2877 Cov.: 31

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.191 AC: 29113 AN: 152042 Hom.: 2873 Cov.: 31 AF XY: 0.195 AC XY: 14512 AN XY: 74326

African (AFR) AF: 0.143 AC: 5920 AN: 41476

American (AMR) AF: 0.192 AC: 2937 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 986 AN: 3470

East Asian (EAS) AF: 0.213 AC: 1098 AN: 5158

South Asian (SAS) AF: 0.399 AC: 1928 AN: 4828

European-Finnish (FIN) AF: 0.184 AC: 1936 AN: 10550

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.201 AC: 13631 AN: 67982

Other (OTH) AF: 0.189 AC: 398 AN: 2104

Alfa AF: 0.205 Hom.: 2870

Bravo AF: 0.185

Asia WGS AF: 0.278 AC: 966 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.7
DANN	Benign	0.86
PhyloP100		-0.098

Splicing

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

Other links and lift over

dbSNP: rs7036795; hg19: chr9-71168318;