NM_001080394.4(SPIDR):c.1361G>A (p.Arg454His) AND not specified

Germline classification:: Likely benign (1 submission)
Last evaluated:: Sep 17, 2021
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:: RCV004130497.1

Allele description [Variation Report for NM_001080394.4(SPIDR):c.1361G>A (p.Arg454His)]

NM_001080394.4(SPIDR):c.1361G>A (p.Arg454His)

Genes:

LOC130000329:ATAC-STARR-seq lymphoblastoid active region 27328 [Gene]
SPIDR:scaffold protein involved in DNA repair [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

8q11.21

Genomic location:

Preferred name:

NM_001080394.4(SPIDR):c.1361G>A (p.Arg454His)

HGVS:

NC_000008.11:g.47599013G>A
NM_001080394.4:c.1361G>AMANE SELECT
NM_001282916.1:c.1151G>A
NM_001282919.1:c.1181G>A
NM_001352931.1:c.1361G>A
NM_001352932.1:c.1241G>A
NM_001352933.1:c.1181G>A
NM_001352934.1:c.1361G>A
NM_001352935.1:c.1151G>A
NM_001352936.1:c.1151G>A
NM_001352937.1:c.1181G>A
NM_001352938.1:c.869G>A
NM_001352939.1:c.869G>A
NM_001352940.1:c.869G>A
NM_001352941.1:c.845G>A
NM_001352942.1:c.704G>A
NM_001352943.1:c.869G>A
NM_001352944.1:c.845G>A
NM_001352945.1:c.635G>A
NM_001352946.1:c.611G>A
NM_001352947.1:c.611G>A
NM_001352948.1:c.611G>A
NM_001352949.1:c.704G>A
NM_001352950.1:c.869G>A
NM_001352951.1:c.611G>A
NM_001352952.1:c.428G>A
NM_001352953.1:c.428G>A
NM_001352955.1:c.428G>A
NM_001352956.1:c.428G>A
NM_001352957.1:c.428G>A
NM_001352958.1:c.113G>A
NM_001352961.1:c.1361G>A
NP_001073863.1:p.Arg454His
NP_001269845.1:p.Arg384His
NP_001269848.1:p.Arg394His
NP_001339860.1:p.Arg454His
NP_001339861.1:p.Arg414His
NP_001339862.1:p.Arg394His
NP_001339863.1:p.Arg454His
NP_001339864.1:p.Arg384His
NP_001339865.1:p.Arg384His
NP_001339866.1:p.Arg394His
NP_001339867.1:p.Arg290His
NP_001339868.1:p.Arg290His
NP_001339869.1:p.Arg290His
NP_001339870.1:p.Arg282His
NP_001339871.1:p.Arg235His
NP_001339872.1:p.Arg290His
NP_001339873.1:p.Arg282His
NP_001339874.1:p.Arg212His
NP_001339875.1:p.Arg204His
NP_001339876.1:p.Arg204His
NP_001339877.1:p.Arg204His
NP_001339878.1:p.Arg235His
NP_001339879.1:p.Arg290His
NP_001339880.1:p.Arg204His
NP_001339881.1:p.Arg143His
NP_001339882.1:p.Arg143His
NP_001339884.1:p.Arg143His
NP_001339885.1:p.Arg143His
NP_001339886.1:p.Arg143His
NP_001339887.1:p.Arg38His
NP_001339890.1:p.Arg454His
NC_000008.10:g.48511575G>A
NM_001080394.2:c.1361G>A
NR_148202.1:n.1442G>A
NR_148203.1:n.1405G>A
NR_148204.1:n.1442G>A
NR_148205.1:n.1442G>A

Protein change:

R143H

Molecular consequence:

NM_001080394.4:c.1361G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001282916.1:c.1151G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001282919.1:c.1181G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001352931.1:c.1361G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001352932.1:c.1241G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001352933.1:c.1181G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001352934.1:c.1361G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001352935.1:c.1151G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001352936.1:c.1151G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001352937.1:c.1181G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001352938.1:c.869G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001352939.1:c.869G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001352940.1:c.869G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001352941.1:c.845G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001352942.1:c.704G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001352943.1:c.869G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001352944.1:c.845G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001352945.1:c.635G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001352946.1:c.611G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001352947.1:c.611G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001352948.1:c.611G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001352949.1:c.704G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001352950.1:c.869G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001352951.1:c.611G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001352952.1:c.428G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001352953.1:c.428G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001352955.1:c.428G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001352956.1:c.428G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001352957.1:c.428G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001352958.1:c.113G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001352961.1:c.1361G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_148202.1:n.1442G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148203.1:n.1405G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148204.1:n.1442G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148205.1:n.1442G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003613832	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely benign (Sep 17, 2021)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003613832

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Likely benign
(Sep 17, 2021)

germline

clinical testing

Citation Link

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

Details of each submission

From Ambry Genetics, SCV003613832.2

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

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

#	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: Nov 24, 2024

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Relating variation to medicine