rs121918415
Positions:
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The ENST00000274576.9(GLRA1):c.690C>T(p.Tyr230=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000041 in 1,461,824 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000041 ( 0 hom. )
Consequence
GLRA1
ENST00000274576.9 synonymous
ENST00000274576.9 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.45
Genes affected
GLRA1 (HGNC:4326): (glycine receptor alpha 1) The protein encoded by this gene is a subunit of a pentameric inhibitory glycine receptor, which mediates postsynaptic inhibition in the central nervous system. Defects in this gene are a cause of startle disease (STHE), also known as hereditary hyperekplexia or congenital stiff-person syndrome. Multiple transcript variants encoding different isoforms have been found. [provided by RefSeq, Dec 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BP6
Variant 5-151855047-G-A is Benign according to our data. Variant chr5-151855047-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1912166.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=2.45 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GLRA1 | NM_000171.4 | c.690C>T | p.Tyr230= | synonymous_variant | 6/9 | ENST00000274576.9 | NP_000162.2 | |
GLRA1 | NM_001146040.2 | c.690C>T | p.Tyr230= | synonymous_variant | 6/9 | NP_001139512.1 | ||
GLRA1 | NM_001292000.2 | c.441C>T | p.Tyr147= | synonymous_variant | 5/8 | NP_001278929.1 | ||
GLRA1 | XM_047417105.1 | c.738C>T | p.Tyr246= | synonymous_variant | 6/9 | XP_047273061.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GLRA1 | ENST00000274576.9 | c.690C>T | p.Tyr230= | synonymous_variant | 6/9 | 1 | NM_000171.4 | ENSP00000274576 | P4 | |
GLRA1 | ENST00000455880.2 | c.690C>T | p.Tyr230= | synonymous_variant | 6/9 | 1 | ENSP00000411593 | A1 | ||
GLRA1 | ENST00000471351.2 | n.973C>T | non_coding_transcript_exon_variant | 6/8 | 1 | |||||
GLRA1 | ENST00000462581.6 | c.*448C>T | 3_prime_UTR_variant, NMD_transcript_variant | 5/8 | 1 | ENSP00000430595 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461824Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 4AN XY: 727218
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1461824
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AN XY:
727218
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GnomAD4 genome Cov.: 32
GnomAD4 genome
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32
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Hereditary hyperekplexia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | May 12, 2022 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at