Variant rs73001406 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000531328.2(TREHP1):n.216-23C>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 0.227 in 473,236 control chromosomes in the GnomAD database, including 13,122 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 0.21 ( 3396 hom., cov: 32)

Exomes 𝑓: 0.24 ( 9726 hom. )

Consequence

TREHP1
ENST00000531328.2 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.678

Variant links:

Genes affected

TREHP1 (HGNC:51907): (trehalase pseudogene 1)

TREHP1 links:

LOC105369519 (HGNC:):

LOC105369519 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369519	XR_007062909.1 linkuse as main transcript	n.87+513G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TREHP1	ENST00000531328.2 linkuse as main transcript	n.216-23C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.206

AC:

31267

AN:

152090

Hom.:

3389

Cov.:

show subpopulations

Gnomad AFR

AF:

0.135

Gnomad AMI

AF:

0.177

Gnomad AMR

AF:

0.207

Gnomad ASJ

AF:

0.200

Gnomad EAS

AF:

0.268

Gnomad SAS

AF:

0.353

Gnomad FIN

AF:

0.227

Gnomad MID

AF:

0.206

Gnomad NFE

AF:

0.230

Gnomad OTH

AF:

0.198

GnomAD4 exome

AF:

0.237

AC:

76219

AN:

321028

Hom.:

9726

Cov.:

AF XY:

0.245

AC XY:

41702

AN XY:

169916

show subpopulations

Gnomad4 AFR exome

AF:

0.134

Gnomad4 AMR exome

AF:

0.188

Gnomad4 ASJ exome

AF:

0.199

Gnomad4 EAS exome

AF:

0.251

Gnomad4 SAS exome

AF:

0.336

Gnomad4 FIN exome

AF:

0.231

Gnomad4 NFE exome

AF:

0.228

Gnomad4 OTH exome

AF:

0.226

GnomAD4 genome

AF:

0.206

AC:

31293

AN:

152208

Hom.:

3396

Cov.:

AF XY:

0.208

AC XY:

15489

AN XY:

74408

show subpopulations

Gnomad4 AFR

AF:

0.135

Gnomad4 AMR

AF:

0.207

Gnomad4 ASJ

AF:

0.200

Gnomad4 EAS

AF:

0.268

Gnomad4 SAS

AF:

0.355

Gnomad4 FIN

AF:

0.227

Gnomad4 NFE

AF:

0.230

Gnomad4 OTH

AF:

0.199

Alfa

AF:

0.215

Hom.:

464

Bravo

AF:

0.195

Asia WGS

AF:

0.280

AC:

972

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.97

DANN

Benign

0.84

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over