NM_012388.4(BLOC1S6):c.82+10A>G AND Hermansky-Pudlak syndrome 9

Germline classification:: Benign/Likely benign (2 submissions)
Last evaluated:: Jan 29, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000625163.11

Allele description [Variation Report for NM_012388.4(BLOC1S6):c.82+10A>G]

NM_012388.4(BLOC1S6):c.82+10A>G

Gene:

BLOC1S6:biogenesis of lysosomal organelles complex 1 subunit 6 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

15q21.1

Genomic location:

Preferred name:

NM_012388.4(BLOC1S6):c.82+10A>G

HGVS:

NC_000015.10:g.45587535A>G
NG_028194.2:g.5317A>G
NM_012388.4:c.82+10A>GMANE SELECT
LRG_883t1:c.82+10A>G
LRG_883:g.5317A>G
NC_000015.9:g.45879733A>G
NM_012388.3:c.82+10A>G

Links:

dbSNP: rs370370639

NCBI 1000 Genomes Browser:

rs370370639

Molecular consequence:

NM_012388.4:c.82+10A>G - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: Hermansky-Pudlak syndrome 9 (HPS9)
Identifiers:: MONDO: MONDO:0013606; MedGen: C3280026; Orphanet: 280663; Orphanet: 79430; OMIM: 614171

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000743954	Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus	criteria provided, single submitter (ACGS Guidelines, 2013)	Likely benign (Oct 30, 2017)	germline	clinical testing	Citation Link,
SCV000771319	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Jan 29, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000743954

Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus

criteria provided, single submitter

(ACGS Guidelines, 2013)

Likely benign
(Oct 30, 2017)

germline

clinical testing

Citation Link,

SCV000771319

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Benign
(Jan 29, 2024)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus, SCV000743954.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000771319.7

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 13, 2024

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