rs33954285
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_019859.4(HTR7):c.1343C>T(p.Pro448Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000527 in 1,613,792 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P448Q) has been classified as Likely benign.
Frequency
Consequence
NM_019859.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HTR7 | NM_019859.4 | c.1343C>T | p.Pro448Leu | missense_variant | Exon 3 of 4 | ENST00000336152.8 | NP_062873.1 | |
HTR7 | XM_024447973.2 | c.749C>T | p.Pro250Leu | missense_variant | Exon 3 of 4 | XP_024303741.1 | ||
HTR7 | NM_000872.5 | c.1296-1115C>T | intron_variant | Intron 2 of 2 | NP_000863.1 | |||
HTR7 | NM_019860.4 | c.*2-1115C>T | intron_variant | Intron 2 of 2 | NP_062874.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HTR7 | ENST00000336152.8 | c.1343C>T | p.Pro448Leu | missense_variant | Exon 3 of 4 | 1 | NM_019859.4 | ENSP00000337949.3 | ||
HTR7 | ENST00000277874.10 | c.1296-1115C>T | intron_variant | Intron 2 of 2 | 1 | ENSP00000277874.6 | ||||
HTR7 | ENST00000371719.2 | c.*2-1115C>T | intron_variant | Intron 2 of 2 | 1 | ENSP00000360784.2 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152086Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000107 AC: 27AN: 251380Hom.: 1 AF XY: 0.0000957 AC XY: 13AN XY: 135856
GnomAD4 exome AF: 0.0000547 AC: 80AN: 1461706Hom.: 0 Cov.: 31 AF XY: 0.0000550 AC XY: 40AN XY: 727150
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152086Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74290
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at