chr20-62216312-G-A
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_007232.3(HRH3):c.1032C>T(p.Phe344=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000682 in 1,610,404 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0036 ( 7 hom., cov: 33)
Exomes 𝑓: 0.00038 ( 4 hom. )
Consequence
HRH3
NM_007232.3 synonymous
NM_007232.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.20
Genes affected
HRH3 (HGNC:5184): (histamine receptor H3) 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. This gene encodes one of the histamine receptors (H3) which belongs to the family 1 of G protein-coupled receptors. It is an integral membrane protein and can regulate neurotransmitter release. This receptor can also increase voltage-dependent calcium current in smooth muscles and innervates the blood vessels and the heart in cardiovascular system. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
Variant 20-62216312-G-A is Benign according to our data. Variant chr20-62216312-G-A is described in ClinVar as [Benign]. Clinvar id is 786973.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAd4 at 7 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HRH3 | NM_007232.3 | c.1032C>T | p.Phe344= | synonymous_variant | 3/3 | ENST00000340177.10 | |
HRH3 | XM_005260266.4 | c.1032C>T | p.Phe344= | synonymous_variant | 3/4 | ||
HRH3 | XM_017027623.2 | c.990C>T | p.Phe330= | synonymous_variant | 3/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HRH3 | ENST00000340177.10 | c.1032C>T | p.Phe344= | synonymous_variant | 3/3 | 1 | NM_007232.3 | P1 | |
HRH3 | ENST00000317393.10 | c.822-30C>T | intron_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.00358 AC: 545AN: 152226Hom.: 7 Cov.: 33
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GnomAD3 exomes AF: 0.000897 AC: 220AN: 245340Hom.: 2 AF XY: 0.000540 AC XY: 72AN XY: 133338
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GnomAD4 exome AF: 0.000379 AC: 553AN: 1458060Hom.: 4 Cov.: 30 AF XY: 0.000313 AC XY: 227AN XY: 724990
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GnomAD4 genome AF: 0.00358 AC: 545AN: 152344Hom.: 7 Cov.: 33 AF XY: 0.00340 AC XY: 253AN XY: 74504
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Apr 10, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at