chr1-31619569-A-G
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001525.3(HCRTR1):c.237A>G(p.Thr79=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00419 in 1,614,126 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0031 ( 2 hom., cov: 33)
Exomes 𝑓: 0.0043 ( 12 hom. )
Consequence
HCRTR1
NM_001525.3 synonymous
NM_001525.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -4.57
Genes affected
HCRTR1 (HGNC:4848): (hypocretin receptor 1) The protein encoded by this gene is a G-protein coupled receptor involved in the regulation of feeding behavior. The encoded protein selectively binds the hypothalamic neuropeptide orexin A. A related gene (HCRTR2) encodes a G-protein coupled receptor that binds orexin A and orexin B. [provided by RefSeq, Jan 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BP6
?
Variant 1-31619569-A-G is Benign according to our data. Variant chr1-31619569-A-G is described in ClinVar as [Benign]. Clinvar id is 779395.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-4.57 with no splicing effect.
BS2
?
High Homozygotes in GnomAd at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HCRTR1 | NM_001525.3 | c.237A>G | p.Thr79= | synonymous_variant | 4/9 | ENST00000403528.7 | |
HCRTR1 | XM_024446605.2 | c.237A>G | p.Thr79= | synonymous_variant | 5/11 | ||
HCRTR1 | XM_017001107.2 | c.237A>G | p.Thr79= | synonymous_variant | 2/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HCRTR1 | ENST00000403528.7 | c.237A>G | p.Thr79= | synonymous_variant | 4/9 | 5 | NM_001525.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00308 AC: 469AN: 152194Hom.: 2 Cov.: 33
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GnomAD3 exomes AF: 0.00362 AC: 908AN: 251136Hom.: 2 AF XY: 0.00361 AC XY: 490AN XY: 135786
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GnomAD4 exome AF: 0.00431 AC: 6302AN: 1461814Hom.: 12 Cov.: 33 AF XY: 0.00421 AC XY: 3065AN XY: 727214
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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 | May 30, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at