rs723867
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_013381.3(TRHDE):c.1723-124G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 586,744 control chromosomes in the GnomAD database, including 35,676 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 0.40 ( 14654 hom., cov: 32)
Exomes 𝑓: 0.29 ( 21022 hom. )
Consequence
TRHDE
NM_013381.3 intron
NM_013381.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.81
Genes affected
TRHDE (HGNC:30748): (thyrotropin releasing hormone degrading enzyme) This gene encodes a member of the peptidase M1 family. The encoded protein is an extracellular peptidase that specifically cleaves and inactivates the neuropeptide thyrotropin-releasing hormone.[provided by RefSeq, Dec 2008]
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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=-0.93).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRHDE | NM_013381.3 | c.1723-124G>C | intron_variant | ENST00000261180.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRHDE | ENST00000261180.10 | c.1723-124G>C | intron_variant | 1 | NM_013381.3 | P1 | |||
TRHDE | ENST00000547300.2 | c.1189-124G>C | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.401 AC: 60436AN: 150888Hom.: 14611 Cov.: 32
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GnomAD4 exome AF: 0.294 AC: 128174AN: 435736Hom.: 21022 AF XY: 0.291 AC XY: 65206AN XY: 223782
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GnomAD4 genome ? AF: 0.401 AC: 60524AN: 151008Hom.: 14654 Cov.: 32 AF XY: 0.400 AC XY: 29470AN XY: 73756
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at