chr1-19666215-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_000871.3(HTR6):c.462C>T(p.Ala154=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00532 in 1,609,212 control chromosomes in the GnomAD database, including 35 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0034 ( 2 hom., cov: 32)
Exomes 𝑓: 0.0055 ( 33 hom. )
Consequence
HTR6
NM_000871.3 synonymous
NM_000871.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.39
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 -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.5).
BP6
?
Variant 1-19666215-C-T is Benign according to our data. Variant chr1-19666215-C-T is described in ClinVar as [Benign]. Clinvar id is 716797.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.39 with no splicing effect.
BS2
?
High Homozygotes in GnomAd at 2 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HTR6 | NM_000871.3 | c.462C>T | p.Ala154= | synonymous_variant | 1/3 | ENST00000289753.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HTR6 | ENST00000289753.2 | c.462C>T | p.Ala154= | synonymous_variant | 1/3 | 1 | NM_000871.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00336 AC: 512AN: 152224Hom.: 2 Cov.: 32
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GnomAD3 exomes AF: 0.00273 AC: 672AN: 245772Hom.: 4 AF XY: 0.00264 AC XY: 353AN XY: 133568
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GnomAD4 exome AF: 0.00552 AC: 8041AN: 1456870Hom.: 33 Cov.: 33 AF XY: 0.00528 AC XY: 3826AN XY: 724948
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GnomAD4 genome ? AF: 0.00336 AC: 512AN: 152342Hom.: 2 Cov.: 32 AF XY: 0.00306 AC XY: 228AN XY: 74500
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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 | Jul 11, 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