chr5-148476770-G-C
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000521530.6(HTR4):c.1077-25498C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,594 control chromosomes in the GnomAD database, with no homozygous occurrence. 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
Consequence
ENST00000521530.6 intron
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HTR4 | NM_001040169.2 | c.1077-25498C>G | intron_variant | Intron 5 of 5 | NP_001035259.1 | |||
HTR4 | NM_199453.3 | c.1077-10845C>G | intron_variant | Intron 5 of 6 | NP_955525.1 | |||
HTR4 | NM_001040172.2 | c.1077-25C>G | intron_variant | Intron 5 of 5 | NP_001035262.2 | |||
LOC107986462 | XR_001742935.2 | n.441+7753G>C | intron_variant | Intron 2 of 3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HTR4 | ENST00000521530.6 | c.1077-25498C>G | intron_variant | Intron 6 of 6 | 1 | ENSP00000428320.1 | ||||
HTR4 | ENST00000521735.5 | c.1077-10845C>G | intron_variant | Intron 5 of 6 | 1 | ENSP00000430979.1 | ||||
HTR4 | ENST00000517929.5 | c.1077-25C>G | intron_variant | Intron 5 of 5 | 1 | ENSP00000435904.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD2 exomes AF: 0.00000408 AC: 1AN: 245090 AF XY: 0.00 show subpopulations
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460594Hom.: 0 Cov.: 35 AF XY: 0.00 AC XY: 0AN XY: 726576 show subpopulations
Age Distribution
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at