rs13064530
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000431010.3(HRH1):c.-35-34775G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 152,046 control chromosomes in the GnomAD database, including 4,603 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 0.24 ( 4603 hom., cov: 32)
Consequence
HRH1
ENST00000431010.3 intron
ENST00000431010.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.314
Genes affected
HRH1 (HGNC:5182): (histamine receptor H1) Histamine is a ubiquitous messenger molecule released from mast cells, enterochromaffin-like cells, and neurons. Its various actions are mediated by histamine receptors H1, H2, H3 and H4. The protein encoded by this gene is an integral membrane protein and belongs to the G protein-coupled receptor superfamily. It mediates the contraction of smooth muscles, the increase in capillary permeability due to contraction of terminal venules, the release of catecholamine from adrenal medulla, and neurotransmission in the central nervous system. It has been associated with multiple processes, including memory and learning, circadian rhythm, and thermoregulation. It is also known to contribute to the pathophysiology of allergic diseases such as atopic dermatitis, asthma, anaphylaxis and allergic rhinitis. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Jan 2015]
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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=-0.76).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HRH1 | NM_001098212.2 | c.-35-34775G>A | intron_variant | ENST00000431010.3 | NP_001091682.1 | |||
LOC102723663 | XR_001740596.2 | n.219+1472C>T | intron_variant, non_coding_transcript_variant | |||||
HRH1 | NM_001098213.2 | c.-35-34775G>A | intron_variant | NP_001091683.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HRH1 | ENST00000431010.3 | c.-35-34775G>A | intron_variant | 1 | NM_001098212.2 | ENSP00000397028 | P1 | |||
ENST00000648436.1 | n.178+1472C>T | intron_variant, non_coding_transcript_variant | ||||||||
HRH1 | ENST00000438284.2 | c.-35-34775G>A | intron_variant | 2 | ENSP00000406705 | P1 | ||||
ENST00000658562.1 | n.144+1468C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.244 AC: 37143AN: 151928Hom.: 4598 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: 0.245 AC: 37180AN: 152046Hom.: 4603 Cov.: 32 AF XY: 0.243 AC XY: 18048AN XY: 74326
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1212
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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