rs10573454

Variant names:

• chr22-26451986-ACGCGCGCGCGCGCGCG-A
• rs10573454
• NM_022081.6:c.*1231_*1246delCGCGCGCGCGCGCGCG

Your query was ambiguous. Multiple possible variants found:

• chr22-26451986-ACGCGCGCGCGCGCGCG-A
• chr22-26451986-ACGCGCGCGCGCGCGCG-ACG
• chr22-26451986-ACGCGCGCGCGCGCGCG-ACGCG
• chr22-26451986-ACGCGCGCGCGCGCGCG-ACGCGCG
• chr22-26451986-ACGCGCGCGCGCGCGCG-ACGCGCGCG
• chr22-26451986-ACGCGCGCGCGCGCGCG-ACGCGCGCGCG
• chr22-26451986-ACGCGCGCGCGCGCGCG-ACGCGCGCGCGCG
• chr22-26451986-ACGCGCGCGCGCGCGCG-ACGCGCGCGCGCGCG
• chr22-26451986-ACGCGCGCGCGCGCGCG-ACGCGCGCGCGCGCGCGCG
• chr22-26451986-ACGCGCGCGCGCGCGCG-ACGCGCGCGCGCGCGCGCGCG
• chr22-26451986-ACGCGCGCGCGCGCGCG-ACGCGCGCGCGCGCGCGCGCGCG
• chr22-26451986-ACGCGCGCGCGCGCGCG-ACGCGCGCGCGCGCGCGCGCGCGCG

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_022081.6(HPS4):​c.*1231_*1246delCGCGCGCGCGCGCGCG variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.0000074 (0 hom., cov: 0)
• Consequence: HPS4 NM_022081.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.278

Genes affected

HPS4 (HGNC:15844): (HPS4 biogenesis of lysosomal organelles complex 3 subunit 2) This gene encodes a protein component of biogenesis of lysosome-related organelles complexes (BLOC). BLOC complexes are important for the formation of endosomal-lysosomal organelles such as melanosomes and platelet dense granules. Mutations in this gene result in subtype 4 of Hermansky-Pudlak syndrome, a form of albinism. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2012]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HPS4	NM_022081.6	c.*1231_*1246delCGCGCGCGCGCGCGCG		3_prime_UTR_variant	Exon 14 of 14	ENST00000398145.7	NP_071364.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HPS4	ENST00000398145	c.*1231_*1246delCGCGCGCGCGCGCGCG		3_prime_UTR_variant	Exon 14 of 14	1	NM_022081.6	ENSP00000381213.2

Frequencies

GnomAD3 genomes AF: 0.00000742 AC: 1 AN: 134760 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000221

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.00000742 AC: 1 AN: 134760 Hom.: 0 Cov.: 0 AF XY: 0.0000154 AC XY: 1 AN XY: 65008

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000221

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10573454; hg19: chr22-26847952;