rs1421125
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_021624.4(HRH4):c.*385G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 161,962 control chromosomes in the GnomAD database, including 8,716 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 0.31 ( 8090 hom., cov: 34)
Exomes 𝑓: 0.34 ( 626 hom. )
Consequence
HRH4
NM_021624.4 3_prime_UTR
NM_021624.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.867
Genes affected
HRH4 (HGNC:17383): (histamine receptor H4) Histamine is a ubiquitous messenger molecule released from mast cells, enterochromaffin-like cells, and neurons. Its various actions are mediated by a family of histamine receptors, which are a subset of the G-protein coupled receptor superfamily. This gene encodes a histamine receptor that is predominantly expressed in haematopoietic cells. The protein is thought to play a role in inflammation and allergy reponses. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2009]
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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=-0.86).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HRH4 | NM_021624.4 | c.*385G>T | 3_prime_UTR_variant | 3/3 | ENST00000256906.5 | ||
HRH4 | NM_001143828.2 | c.*385G>T | 3_prime_UTR_variant | 2/2 | |||
HRH4 | NM_001160166.2 | c.*1190G>T | 3_prime_UTR_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HRH4 | ENST00000256906.5 | c.*385G>T | 3_prime_UTR_variant | 3/3 | 1 | NM_021624.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.313 AC: 47667AN: 152096Hom.: 8092 Cov.: 34
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GnomAD4 exome AF: 0.344 AC: 3352AN: 9746Hom.: 626 Cov.: 0 AF XY: 0.348 AC XY: 1823AN XY: 5240
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GnomAD4 genome ? AF: 0.313 AC: 47665AN: 152216Hom.: 8090 Cov.: 34 AF XY: 0.309 AC XY: 23015AN XY: 74412
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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