chrX-14690691-G-GTCTC
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_002063.4(GLRA2):c.931-6_931-3dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000396 in 924,774 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 78 hemizygotes in GnomAD. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00035 ( 0 hom., 9 hem., cov: 23)
Exomes 𝑓: 0.00040 ( 0 hom. 69 hem. )
Consequence
GLRA2
NM_002063.4 intron
NM_002063.4 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.590
Genes affected
GLRA2 (HGNC:4327): (glycine receptor alpha 2) The glycine receptor consists of two subunits, alpha and beta, and acts as a pentamer. The protein encoded by this gene is an alpha subunit and can bind strychnine. Several transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jan 2010]
FANCB (HGNC:3583): (FA complementation group B) This gene encodes a member of the Fanconi anemia complementation group B. This protein is assembled into a nucleoprotein complex that is involved in the repair of DNA lesions. Mutations in this gene can cause chromosome instability and VACTERL syndrome with hydrocephalus. [provided by RefSeq, Apr 2016]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP6
?
Variant X-14690691-G-GTCTC is Benign according to our data. Variant chrX-14690691-G-GTCTC is described in ClinVar as [Likely_benign]. Clinvar id is 3054739.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Hemizygotes in GnomAd at 9 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GLRA2 | NM_002063.4 | c.931-6_931-3dup | intron_variant | ENST00000218075.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLRA2 | ENST00000218075.9 | c.931-6_931-3dup | intron_variant | 1 | NM_002063.4 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.000348 AC: 38AN: 109130Hom.: 0 Cov.: 23 AF XY: 0.000283 AC XY: 9AN XY: 31858
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GnomAD3 exomes AF: 0.000314 AC: 39AN: 124260Hom.: 0 AF XY: 0.000257 AC XY: 10AN XY: 38956
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GnomAD4 exome AF: 0.000402 AC: 328AN: 815601Hom.: 0 Cov.: 15 AF XY: 0.000290 AC XY: 69AN XY: 237923
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
GLRA2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 26, 2020 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at