9-68614263-A-G

Variant summary

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

The ENST00000413269.3(TMEM252-DT):n.461-11378A>G 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 0.611 in 151,848 control chromosomes in the GnomAD database, including 28,815 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 (28815 hom., cov: 31)
• Consequence: TMEM252-DT ENST00000413269.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.460

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM252-DT	XR_007061564.1	n.1662-18772A>G		intron_variant, non_coding_transcript_variant
TMEM252-DT	XR_001746701.3	n.515-11378A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM252-DT	ENST00000413269.3	n.461-11378A>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.611 AC: 92721 AN: 151730 Hom.: 28811 Cov.: 31

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.703

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.611 AC: 92769 AN: 151848 Hom.: 28815 Cov.: 31 AF XY: 0.610 AC XY: 45271 AN XY: 74190

Gnomad4 AFR AF: 0.548

Gnomad4 AMR AF: 0.503

Gnomad4 ASJ AF: 0.632

Gnomad4 EAS AF: 0.414

Gnomad4 SAS AF: 0.645

Gnomad4 FIN AF: 0.703

Gnomad4 NFE AF: 0.668

Gnomad4 OTH AF: 0.623

Alfa AF: 0.646 Hom.: 44060

Bravo AF: 0.587

Asia WGS AF: 0.538 AC: 1871 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.0
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7864204; hg19: chr9-71229179;