rs1894706
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_022081.6(HPS4):c.1816C>T(p.His606Tyr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.909 in 1,613,888 control chromosomes in the GnomAD database, including 670,648 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. H606H) has been classified as Likely benign.
Frequency
Consequence
NM_022081.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HPS4 | NM_022081.6 | c.1816C>T | p.His606Tyr | missense_variant | 12/14 | ENST00000398145.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HPS4 | ENST00000398145.7 | c.1816C>T | p.His606Tyr | missense_variant | 12/14 | 1 | NM_022081.6 | P2 |
Frequencies
GnomAD3 genomes AF: 0.865 AC: 131482AN: 151944Hom.: 57479 Cov.: 30
GnomAD3 exomes AF: 0.877 AC: 220435AN: 251290Hom.: 97959 AF XY: 0.890 AC XY: 120857AN XY: 135826
GnomAD4 exome AF: 0.914 AC: 1336049AN: 1461828Hom.: 613157 Cov.: 61 AF XY: 0.916 AC XY: 666301AN XY: 727212
GnomAD4 genome AF: 0.865 AC: 131542AN: 152060Hom.: 57491 Cov.: 30 AF XY: 0.865 AC XY: 64319AN XY: 74332
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Feb 21, 2013 | His606Tyr in exon 12 of HPS4: This variant is not expected to have clinical sign ificance because it has been identified in 24.6% (1084/4406) of African American chromosomes from a broad population by the NHLBI Exome Sequencing Project (http ://evs.gs.washington.edu/EVS; dbSNP rs1894706). - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Hermansky-Pudlak syndrome 4 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Aug 10, 2021 | - - |
Hermansky-Pudlak syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at