NM_032122.5(DTNBP1):c.162G>A (p.Arg54=) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 28, 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:: RCV001852553.3

Allele description [Variation Report for NM_032122.5(DTNBP1):c.162G>A (p.Arg54=)]

NM_032122.5(DTNBP1):c.162G>A (p.Arg54=)

Gene:

DTNBP1:dystrobrevin binding protein 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

6p22.3

Genomic location:

Preferred name:

NM_032122.5(DTNBP1):c.162G>A (p.Arg54=)

HGVS:

NC_000006.12:g.15637804C>T
NG_009309.1:g.30237G>A
NM_001271667.2:c.-82G>A
NM_001271668.2:c.111G>A
NM_001271669.2:c.57G>A
NM_032122.5:c.162G>AMANE SELECT
NM_183040.2:c.162G>A
NP_001258597.1:p.Arg37=
NP_001258598.1:p.Gly19=
NP_115498.2:p.Arg54=
NP_115498.2:p.Arg54=
NP_898861.1:p.Arg54=
LRG_588t1:c.162G>A
LRG_588t2:c.162G>A
LRG_588:g.30237G>A
LRG_588p1:p.Arg54=
LRG_588p2:p.Arg54=
NC_000006.11:g.15638035C>T
NM_032122.4:c.162G>A
NR_036448.3:n.460G>A

Links:

dbSNP: rs77460377

NCBI 1000 Genomes Browser:

rs77460377

Molecular consequence:

NM_001271667.2:c.-82G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NR_036448.3:n.460G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001271668.2:c.111G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001271669.2:c.57G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_032122.5:c.162G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_183040.2:c.162G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002278108	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 28, 2022)	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

SCV002278108

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 28, 2022)

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

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):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV002278108.2

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

Description

This sequence change affects codon 54 of the DTNBP1 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the DTNBP1 protein. It affects a nucleotide within the consensus splice site. This variant is present in population databases (rs77460377, gnomAD 0.1%), and has an allele count higher than expected for a pathogenic variant. This variant has not been reported in the literature in individuals affected with DTNBP1-related conditions. ClinVar contains an entry for this variant (Variation ID: 210857). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant is not likely to affect RNA splicing. 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.

#	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: Feb 4, 2024

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