chr11-18297633-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_181507.2(HPS5):c.1249C>T(p.Leu417=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,410 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
NM_181507.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HPS5 | NM_181507.2 | c.1249C>T | p.Leu417= | synonymous_variant | 11/23 | ENST00000349215.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HPS5 | ENST00000349215.8 | c.1249C>T | p.Leu417= | synonymous_variant | 11/23 | 1 | NM_181507.2 | P1 | |
HPS5 | ENST00000396253.7 | c.907C>T | p.Leu303= | synonymous_variant | 10/22 | 1 | |||
HPS5 | ENST00000438420.6 | c.907C>T | p.Leu303= | synonymous_variant | 10/22 | 1 | |||
HPS5 | ENST00000531848.1 | c.907C>T | p.Leu303= | synonymous_variant | 10/11 | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251352Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135846
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461410Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727028
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at