chr1-19666296-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2
The NM_000871.3(HTR6):c.543C>T(p.Arg181=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00111 in 1,612,798 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0057 ( 11 hom., cov: 32)
Exomes 𝑓: 0.00063 ( 7 hom. )
Consequence
HTR6
NM_000871.3 synonymous
NM_000871.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.920
Genes affected
HTR6 (HGNC:5301): (5-hydroxytryptamine receptor 6) This gene encodes a protein that belongs to the seven-transmembrane G protein-coupled receptor family of proteins. The encoded protein couples with the Gs alpha subunit and stimulates adenylate cyclase to activate the cyclic AMP-dependent signaling pathway. This receptor is thought to regulate cholinergic neuronal transmission in the brain. Several antidepressants and antipsychotic drugs have a high affinity for this receptor. [provided by RefSeq, Aug 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.37).
BP6
?
Variant 1-19666296-C-T is Benign according to our data. Variant chr1-19666296-C-T is described in ClinVar as [Benign]. Clinvar id is 777324.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.92 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00574 (874/152336) while in subpopulation AFR AF= 0.0198 (824/41572). AF 95% confidence interval is 0.0187. There are 11 homozygotes in gnomad4. There are 401 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 10 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HTR6 | NM_000871.3 | c.543C>T | p.Arg181= | synonymous_variant | 1/3 | ENST00000289753.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HTR6 | ENST00000289753.2 | c.543C>T | p.Arg181= | synonymous_variant | 1/3 | 1 | NM_000871.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00574 AC: 873AN: 152218Hom.: 10 Cov.: 32
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GnomAD3 exomes AF: 0.00161 AC: 400AN: 248308Hom.: 6 AF XY: 0.00108 AC XY: 146AN XY: 134746
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GnomAD4 exome AF: 0.000629 AC: 918AN: 1460462Hom.: 7 Cov.: 33 AF XY: 0.000534 AC XY: 388AN XY: 726642
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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 | Jan 09, 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