NM_206933.4(USH2A):c.10256_10262delinsCATTTGCACTGTGCAGTGA (p.Asn3419_Thr3421delinsThrPheAlaLeuCysSerAsp) AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Dec 22, 2021
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:: RCV000734876.5

Allele description [Variation Report for NM_206933.4(USH2A):c.10256_10262delinsCATTTGCACTGTGCAGTGA (p.Asn3419_Thr3421delinsThrPheAlaLeuCysSerAsp)]

NM_206933.4(USH2A):c.10256_10262delinsCATTTGCACTGTGCAGTGA (p.Asn3419_Thr3421delinsThrPheAlaLeuCysSerAsp)

Gene:

USH2A:usherin [Gene - OMIM - HGNC]

Variant type:

Indel

Cytogenetic location:

1q41

Genomic location:

Preferred name:

NM_206933.4(USH2A):c.10256_10262delinsCATTTGCACTGTGCAGTGA (p.Asn3419_Thr3421delinsThrPheAlaLeuCysSerAsp)

HGVS:

NC_000001.11:g.215786795_215786801delinsTCACTGCACAGTGCAAATG
NG_009497.2:g.641648_641654delinsCATTTGCACTGTGCAGTGA
NM_206933.2:c.10256_10262delACTTTACinsCATTTGCACTGTGCAGTGA
NM_206933.4:c.10256_10262delinsCATTTGCACTGTGCAGTGAMANE SELECT
NP_996816.3:p.Asn3419_Thr3421delinsThrPheAlaLeuCysSerAsp
NC_000001.10:g.215960137_215960143delinsTCACTGCACAGTGCAAATG
NG_009497.1:g.641596_641602delinsCATTTGCACTGTGCAGTGA
NM_206933.4:c.10256_10262delinsCATTTGCACTGTGCAGTGA

Links:

dbSNP: rs1558097546

NCBI 1000 Genomes Browser:

rs1558097546

Molecular consequence:

NM_206933.4:c.10256_10262delinsCATTTGCACTGTGCAGTGA - inframe_indel - [Sequence Ontology: SO:0001820]

Observations:

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
SCV000863054	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL ClinVar v180209 classification definitions)	Uncertain significance (Aug 20, 2018)	germline	clinical testing	Citation Link,
SCV002963008	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 22, 2021)	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

SCV000863054

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL ClinVar v180209 classification definitions)

Uncertain significance
(Aug 20, 2018)

germline

clinical testing

Citation Link,

SCV002963008

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 22, 2021)

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	1	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 Eurofins Ntd Llc (ga), SCV000863054.1

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

From Invitae, SCV002963008.1

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

Description

This variant, c.10256_10262delins19, is a complex sequence change that results in the deletion of 3 and insertion of 7 amino acid(s) in the USH2A protein (p.Asn3419_Thr3421delinsThrPheAlaLeuCysSerAsp). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with USH2A-related conditions. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. 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: Dec 9, 2023

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