rs73001406
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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
ENST00000531328.2 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.678
Genes affected
TREHP1 (HGNC:51907): (trehalase pseudogene 1)
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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 | 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 | n.216-23C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.206 AC: 31267AN: 152090Hom.: 3389 Cov.: 32
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GnomAD4 exome AF: 0.237 AC: 76219AN: 321028Hom.: 9726 Cov.: 3 AF XY: 0.245 AC XY: 41702AN XY: 169916
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GnomAD4 genome ? AF: 0.206 AC: 31293AN: 152208Hom.: 3396 Cov.: 32 AF XY: 0.208 AC XY: 15489AN XY: 74408
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at