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NM_001159699.2(FHL1):c.871G>A (p.Asp291Asn) AND not specified

Germline classification:
Benign (6 submissions)
Last evaluated:
Apr 29, 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:
RCV000296313.18

Allele description [Variation Report for NM_001159699.2(FHL1):c.871G>A (p.Asp291Asn)]

NM_001159699.2(FHL1):c.871G>A (p.Asp291Asn)

Gene:
FHL1:four and a half LIM domains 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xq26.3
Genomic location:
Preferred name:
NM_001159699.2(FHL1):c.871G>A (p.Asp291Asn)
HGVS:
  • NC_000023.11:g.136210005G>A
  • NG_015895.1:g.67606G>A
  • NM_001159699.2:c.871G>AMANE SELECT
  • NM_001159700.2:c.823G>A
  • NM_001159701.2:c.910G>A
  • NM_001159702.3:c.*51G>A
  • NM_001159703.2:c.*51G>A
  • NM_001159704.1:c.823G>A
  • NM_001167819.1:c.823G>A
  • NM_001330659.2:c.*51G>A
  • NM_001369326.1:c.*51G>A
  • NM_001369327.2:c.*51G>A
  • NM_001369328.1:c.*51G>A
  • NM_001369329.1:c.823G>A
  • NM_001369330.1:c.823G>A
  • NM_001369331.1:c.823G>A
  • NM_001449.5:c.823G>A
  • NP_001153171.1:p.Asp291Asn
  • NP_001153172.1:p.Asp275Asn
  • NP_001153173.1:p.Asp304Asn
  • NP_001153176.1:p.Asp275Asn
  • NP_001161291.1:p.Asp275Asn
  • NP_001356258.1:p.Asp275Asn
  • NP_001356259.1:p.Asp275Asn
  • NP_001356260.1:p.Asp275Asn
  • NP_001440.2:p.Asp275Asn
  • LRG_739t1:c.871G>A
  • LRG_739t2:c.*51G>A
  • LRG_739:g.67606G>A
  • LRG_739p1:p.Asp291Asn
  • NC_000023.10:g.135292164G>A
  • NM_001159702.2:c.*51G>A
  • NM_001449.4:c.823G>A
  • NR_027621.2:n.1234G>A
Protein change:
D275N
Links:
dbSNP: rs151315725
NCBI 1000 Genomes Browser:
rs151315725
Molecular consequence:
  • NM_001159702.3:c.*51G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001159703.2:c.*51G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001330659.2:c.*51G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001369326.1:c.*51G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001369327.2:c.*51G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001369328.1:c.*51G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001159699.2:c.871G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001159700.2:c.823G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001159701.2:c.910G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001159704.1:c.823G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001167819.1:c.823G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369329.1:c.823G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369330.1:c.823G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369331.1:c.823G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001449.5:c.823G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NR_027621.2:n.1234G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Observations:
1

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000336163Eurofins Ntd Llc (ga)
criteria provided, single submitter

(EGL Classification Definitions 2015)
Benign
(Dec 3, 2015)
germlineclinical testing

Citation Link,

SCV000522548GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))
Benign
(Mar 4, 2016)
germlineclinical testing

Citation Link,

SCV001623250Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)
Benign
(Apr 29, 2021)
germlineclinical testing

Citation Link,

SCV001921766Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus

See additional submitters

no assertion criteria provided
Benigngermlineclinical testing

SCV001930630Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus

See additional submitters

no assertion criteria provided
Benigngermlineclinical testing

SCV001965230Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus

See additional submitters

no assertion criteria provided
Benigngermlineclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown1not providednot providednot providednot providedclinical testing
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Eurofins Ntd Llc (ga), SCV000336163.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided1not providednot providednot provided

From GeneDx, SCV000522548.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV001623250.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Variant summary: FHL1 c.*51G>A is located in the untranslated mRNA region downstream of the termination codon. The variant allele was found at a frequency of 0.011 in 183528 control chromosomes in the gnomAD database, including 17 homozygotes. The observed variant frequency is approximately 28 fold of the estimated maximal expected allele frequency for a pathogenic variant in FHL1 causing Emery-Dreifuss Muscular Dystrophy phenotype (0.00039), strongly suggesting that the variant is benign. To our knowledge, no occurrence of c.*51G>A in individuals affected with Emery-Dreifuss Muscular Dystrophy and no experimental evidence demonstrating its impact on protein function have been reported. Five clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as benign. Based on the evidence outlined above, the variant was classified as benign.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus, SCV001921766.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus, SCV001930630.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus, SCV001965230.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024