5-148484289-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_000870.7(HTR4):c.1077-996A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000718 in 1,613,718 control chromosomes in the GnomAD database, including 15 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0041 ( 9 hom., cov: 32)
Exomes 𝑓: 0.00036 ( 6 hom. )
Consequence
HTR4
NM_000870.7 intron
NM_000870.7 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.262
Genes affected
HTR4 (HGNC:5299): (5-hydroxytryptamine receptor 4) This gene is a member of the family of serotonin receptors, which are G protein coupled receptors that stimulate cAMP production in response to serotonin (5-hydroxytryptamine). The gene product is a glycosylated transmembrane protein that functions in both the peripheral and central nervous system to modulate the release of various neurotransmitters. Multiple transcript variants encoding proteins with distinct C-terminal sequences have been described. [provided by RefSeq, May 2010]
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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=-0.92).
BP6
?
Variant 5-148484289-T-C is Benign according to our data. Variant chr5-148484289-T-C is described in ClinVar as [Benign]. Clinvar id is 780569.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAd at 9 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HTR4 | NM_000870.7 | c.1077-996A>G | intron_variant | ENST00000377888.8 | |||
LOC107986462 | XR_001742935.2 | n.441+15272T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HTR4 | ENST00000377888.8 | c.1077-996A>G | intron_variant | 1 | NM_000870.7 |
Frequencies
GnomAD3 genomes ? AF: 0.00413 AC: 629AN: 152186Hom.: 9 Cov.: 32
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GnomAD3 exomes AF: 0.00104 AC: 260AN: 250856Hom.: 3 AF XY: 0.000797 AC XY: 108AN XY: 135588
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GnomAD4 exome AF: 0.000361 AC: 527AN: 1461414Hom.: 6 Cov.: 30 AF XY: 0.000323 AC XY: 235AN XY: 727026
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GnomAD4 genome ? AF: 0.00414 AC: 631AN: 152304Hom.: 9 Cov.: 32 AF XY: 0.00402 AC XY: 299AN XY: 74462
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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 | Mar 30, 2018 | - - |
Computational scores
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Name
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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