9-68569853-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000413269.3(TMEM252-DT):n.460+27211C>T 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 0.607 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
TMEM252-DT	XR_007061564.1	n.1661+27211C>T		intron_variant, non_coding_transcript_variant
TMEM252-DT	XR_001746701.3	n.514+27211C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM252-DT	ENST00000413269.3	n.460+27211C>T		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.312

Gnomad4 AMR AF: 0.716

Gnomad4 ASJ AF: 0.673

Gnomad4 EAS AF: 0.769

Gnomad4 SAS AF: 0.756

Gnomad4 FIN AF: 0.715

Gnomad4 NFE AF: 0.716

Gnomad4 OTH AF: 0.637

Alfa AF: 0.701 Hom.: 63165

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7046236; hg19: chr9-71184769;