chrX-14532376-G-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_002063.4(GLRA2):c.202+4G>T variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000609 in 1,150,340 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.0000089 ( 0 hom., 1 hem., cov: 23)
Exomes 𝑓: 0.0000058 ( 0 hom. 2 hem. )
Consequence
GLRA2
NM_002063.4 splice_donor_region, intron
NM_002063.4 splice_donor_region, intron
Scores
2
Splicing: ADA: 0.00002230
2
Clinical Significance
Conservation
PhyloP100: 0.997
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.56).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GLRA2 | NM_002063.4 | c.202+4G>T | splice_donor_region_variant, intron_variant | ENST00000218075.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLRA2 | ENST00000218075.9 | c.202+4G>T | splice_donor_region_variant, intron_variant | 1 | NM_002063.4 | A1 | |||
GLRA2 | ENST00000355020.9 | c.202+4G>T | splice_donor_region_variant, intron_variant | 1 | P4 | ||||
GLRA2 | ENST00000443437.6 | c.*169+4G>T | splice_donor_region_variant, intron_variant, NMD_transcript_variant | 2 | |||||
GLRA2 | ENST00000415367.2 | n.453+4G>T | splice_donor_region_variant, intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00000894 AC: 1AN: 111799Hom.: 0 Cov.: 23 AF XY: 0.0000294 AC XY: 1AN XY: 34053
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GnomAD4 exome AF: 0.00000578 AC: 6AN: 1038541Hom.: 0 Cov.: 21 AF XY: 0.00000636 AC XY: 2AN XY: 314593
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GnomAD4 genome ? AF: 0.00000894 AC: 1AN: 111799Hom.: 0 Cov.: 23 AF XY: 0.0000294 AC XY: 1AN XY: 34053
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2017 | - - |
Computational scores
Source:
Name
Calibrated prediction
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at