rs17783131
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000261180.10(TRHDE):c.1188+39058A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 152,036 control chromosomes in the GnomAD database, including 9,961 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 0.35 ( 9961 hom., cov: 32)
Consequence
TRHDE
ENST00000261180.10 intron
ENST00000261180.10 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0480
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=-0.87).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRHDE | NM_013381.3 | c.1188+39058A>C | intron_variant | ENST00000261180.10 | NP_037513.2 | |||
TRHDE | XM_005268819.6 | c.1188+39058A>C | intron_variant | XP_005268876.3 | ||||
TRHDE | XM_017019243.3 | c.1188+39058A>C | intron_variant | XP_016874732.3 | ||||
TRHDE | XM_017019244.2 | c.144+39058A>C | intron_variant | XP_016874733.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TRHDE | ENST00000261180.10 | c.1188+39058A>C | intron_variant | 1 | NM_013381.3 | ENSP00000261180 | P1 | |||
TRHDE | ENST00000547300.2 | c.1188+39058A>C | intron_variant | 3 | ENSP00000447822 | |||||
TRHDE | ENST00000548156.1 | n.280-51983A>C | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.349 AC: 53060AN: 151916Hom.: 9965 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.349 AC: 53061AN: 152036Hom.: 9961 Cov.: 32 AF XY: 0.346 AC XY: 25737AN XY: 74322
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3478
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