rs7036795

Positions:

• chr9-68553402-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000413269.3(TMEM252-DT):​n.460+10760T>C variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
TMEM252-DT	XR_007061564.1	n.1661+10760T>C		intron_variant, non_coding_transcript_variant
TMEM252-DT	XR_001746701.3	n.514+10760T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM252-DT	ENST00000413269.3	n.460+10760T>C		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.284

Gnomad4 EAS AF: 0.213

Gnomad4 SAS AF: 0.399

Gnomad4 FIN AF: 0.184

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.189

Alfa AF: 0.208 Hom.: 2117

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7036795; hg19: chr9-71168318;