chr5-63961297-G-A
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_000524.4(HTR1A):c.423C>T(p.Pro141=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000465 in 1,614,136 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00061 ( 1 hom., cov: 33)
Exomes 𝑓: 0.00045 ( 3 hom. )
Consequence
HTR1A
NM_000524.4 synonymous
NM_000524.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.37
Genes affected
HTR1A (HGNC:5286): (5-hydroxytryptamine receptor 1A) This gene encodes a G protein-coupled receptor for 5-hydroxytryptamine (serotonin), and belongs to the 5-hydroxytryptamine receptor subfamily. Serotonin has been implicated in a number of physiologic processes and pathologic conditions. Inactivation of this gene in mice results in behavior consistent with an increased anxiety and stress response. Mutation in the promoter of this gene has been associated with menstrual cycle-dependent periodic fevers. [provided by RefSeq, Jun 2012]
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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=-0.52).
BP6
Variant 5-63961297-G-A is Benign according to our data. Variant chr5-63961297-G-A is described in ClinVar as [Benign]. Clinvar id is 746639.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.37 with no splicing effect.
BS2
High AC in GnomAd4 at 93 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HTR1A | NM_000524.4 | c.423C>T | p.Pro141= | synonymous_variant | 1/1 | ENST00000323865.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HTR1A | ENST00000323865.5 | c.423C>T | p.Pro141= | synonymous_variant | 1/1 | NM_000524.4 | P1 | ||
ENST00000502882.1 | n.97-3282C>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.000611 AC: 93AN: 152204Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.00137 AC: 343AN: 250508Hom.: 3 AF XY: 0.00131 AC XY: 178AN XY: 135474
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GnomAD4 exome AF: 0.000450 AC: 658AN: 1461814Hom.: 3 Cov.: 31 AF XY: 0.000444 AC XY: 323AN XY: 727202
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GnomAD4 genome AF: 0.000611 AC: 93AN: 152322Hom.: 1 Cov.: 33 AF XY: 0.000591 AC XY: 44AN XY: 74480
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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 | Dec 31, 2019 | - - |
Computational scores
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BayesDel_noAF
Benign
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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