11-18317774-G-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 2P and 15B. PM2BP4_ModerateBP6_Very_StrongBP7BS1
The NM_181507.2(HPS5):c.85C>A(p.Arg29Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000545 in 1,613,732 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_181507.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000329 AC: 50AN: 152146Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000877 AC: 22AN: 250812Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135534
GnomAD4 exome AF: 0.0000260 AC: 38AN: 1461468Hom.: 0 Cov.: 31 AF XY: 0.0000206 AC XY: 15AN XY: 727000
GnomAD4 genome AF: 0.000328 AC: 50AN: 152264Hom.: 0 Cov.: 32 AF XY: 0.000309 AC XY: 23AN XY: 74442
ClinVar
Submissions by phenotype
not specified Benign:2
- -
Arg29Arg in exon 2 of HPS5: This variant is not expected to have clinical signif icance because it does not alter an amino acid residue and is not located within the splice consensus sequence. It has been identified in 0.1% (5/4398) of Afric an American chromosomes from a broad population by the NHLBI Exome Sequencing Pr oject (http://evs.gs.washington.edu/EVS; dbSNP rs138638048). -
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at