NM_022081.6:c.949_972dupGCTTGTCCAGATGGCAGGAAGGAG
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4
The NM_022081.6(HPS4):c.949_972dupGCTTGTCCAGATGGCAGGAAGGAG(p.Glu324_Asn325insAlaCysProAspGlyArgLysGlu) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000247 in 1,460,290 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_022081.6 conservative_inframe_insertion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HPS4 | NM_022081.6 | c.949_972dupGCTTGTCCAGATGGCAGGAAGGAG | p.Glu324_Asn325insAlaCysProAspGlyArgLysGlu | conservative_inframe_insertion | Exon 11 of 14 | ENST00000398145.7 | NP_071364.4 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251226Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135766
GnomAD4 exome AF: 0.0000247 AC: 36AN: 1460290Hom.: 0 Cov.: 34 AF XY: 0.0000234 AC XY: 17AN XY: 726112
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Hermansky-Pudlak syndrome 4 Pathogenic:1Uncertain:1
The p.Ala317_Glu324dup variant in HPS4 has been reported in 1 individual with Hermansky-Pudlak syndrome 4 (PMID: 11836498, 31898847) and has been identified in 0.008% (9/113628) of European (non-Finnish) chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP ID: rs281865164). Although this variant has been seen in the general population in a heterozygous state, its frequency is low enough to be consistent with a recessive carrier frequency. This variant has also been reported in ClinVar (Variation ID#: 4129) and has been interpreted as pathogenic by OMIM and as a variant of uncertain significance by Invitae. This variant is a duplication of 8 amino acids at position 317 and is not predicted to alter the protein reading-frame. It is unclear if this deletion will impact the protein. In summary, the clinical significance of the p.Ala317_Glu324dup variant is uncertain. ACMG/AMP Criteria applied: PM4, PM2_supporting (Richards 2015). -
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not specified Uncertain:1
Variant summary: HPS4 c.949_972dup24 (p.Ala317_Glu324dup) results in an in-frame duplication that is predicted to duplicate 8 amino acids into the encoded protein. The variant allele was found at a frequency of 4e-05 in 251226 control chromosomes (gnomAD). This frequency is not significantly higher than estimated for a pathogenic variant in HPS4 causing Hermansky-Pudlak Syndrome (4e-05 vs 0.00052), allowing no conclusion about variant significance. c.949_972dup24 has been reported in the literature in related heterozygous individuals affected with Hermansky-Pudlak Syndrome without a second variant identified (Suzuki_2002). These data do not allow any conclusion about variant significance. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publication has been ascertained in the context of this evaluation (PMID: 11836498). Two submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. Both submitters classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance. -
not provided Uncertain:1
This variant, c.949_972dup, results in the insertion of 8 amino acid(s) of the HPS4 protein (p.Ala317_Glu324dup), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs281865164, gnomAD 0.007%). This variant has not been reported in the literature in individuals affected with HPS4-related conditions. ClinVar contains an entry for this variant (Variation ID: 4129). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at