rs2420367
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_019859.4(HTR7):c.540-16832G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.62 in 152,092 control chromosomes in the GnomAD database, including 31,078 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.62 ( 31078 hom., cov: 32)
Consequence
HTR7
NM_019859.4 intron
NM_019859.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0540
Genes affected
HTR7 (HGNC:5302): (5-hydroxytryptamine receptor 7) The neurotransmitter, serotonin, is thought to play a role in various cognitive and behavioral functions. The serotonin receptor encoded by this gene belongs to the superfamily of G protein-coupled receptors and the gene is a candidate locus for involvement in autistic disorder and other neuropsychiatric disorders. Three splice variants have been identified which encode proteins that differ in the length of their carboxy terminal ends. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.861 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HTR7 | NM_019859.4 | c.540-16832G>T | intron_variant | ENST00000336152.8 | |||
HTR7 | NM_000872.5 | c.540-16832G>T | intron_variant | ||||
HTR7 | NM_019860.4 | c.540-16832G>T | intron_variant | ||||
HTR7 | XM_024447973.2 | c.-56+10750G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HTR7 | ENST00000336152.8 | c.540-16832G>T | intron_variant | 1 | NM_019859.4 | ||||
HTR7 | ENST00000277874.10 | c.540-16832G>T | intron_variant | 1 | A1 | ||||
HTR7 | ENST00000371719.2 | c.540-16832G>T | intron_variant | 1 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.620 AC: 94149AN: 151974Hom.: 31025 Cov.: 32
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.620 AC: 94262AN: 152092Hom.: 31078 Cov.: 32 AF XY: 0.618 AC XY: 45944AN XY: 74366
GnomAD4 genome
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32
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45944
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74366
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2216
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at