NM_001021.6(RPS17):c.156-1G>A AND Diamond-Blackfan anemia 4

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Dec 16, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV003111527.3

Allele description [Variation Report for NM_001021.6(RPS17):c.156-1G>A]

NM_001021.6(RPS17):c.156-1G>A

Gene:

RPS17:ribosomal protein S17 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

15q25.2

Genomic location:

Preferred name:

NM_001021.6(RPS17):c.156-1G>A

HGVS:

NC_000015.10:g.82538986C>T
NG_009890.2:g.6559G>A
NM_001021.6:c.156-1G>AMANE SELECT
LRG_1143t1:c.156-1G>A
LRG_1143:g.6559G>A
NC_000015.9:g.82823394C>T

Molecular consequence:

NM_001021.6:c.156-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]

Observations:

Condition(s)

Name:: Diamond-Blackfan anemia 4 (DBA4)
Identifiers:: MONDO: MONDO:0012924; MedGen: C2675860; Orphanet: 124; OMIM: 612527

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003762215	Pediatric Oncology and Hematology Unit, National and Kapodistrian University of Athens	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Dec 16, 2022)	de novo	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

SCV003762215

Pediatric Oncology and Hematology Unit, National and Kapodistrian University of Athens

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Dec 16, 2022)

de novo

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
Greek	de novo	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Pediatric Oncology and Hematology Unit, National and Kapodistrian University of Athens, SCV003762215.2

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

Description

The c.156-1G>A variant in RPS17(NM_001021.6) has been found in a girl with Diamond-Blackfan anemia phenotype and was absent from large population studies. Additionally, family segregation analysis showed that the variant is de novo. The variant is expected to disrupt normal splicing. In summary, this variant meets our criteria to be classified as likely pathogenic, based on the segregation study, absence from controls, and possible aberrant splicing.

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

Last Updated: Nov 11, 2023

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