X-14475333-C-T

Variant names:

• chrX-14475333-C-T
• rs9306749
• XM_047441999.1:c.-111+26055C>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The XM_047441999.1(GLRA2):​c.-111+26055C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.60 (15596 hom., 19423 hem., cov: 24)
  • Failed GnomAD Quality Control
• Consequence: GLRA2 XM_047441999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04
• Publications: 0 publications found

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]

GLRA2 Gene-Disease associations (from GenCC):

• intellectual developmental disorder, X-linked, syndromic, Pilorge type

  Inheritance: XL Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.596 AC: 66288 AN: 111277 Hom.: 15599 Cov.: 24

Gnomad AFR AF: 0.877

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.451

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.539

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.596 AC: 66333 AN: 111329 Hom.: 15596 Cov.: 24 AF XY: 0.579 AC XY: 19423 AN XY: 33547

African (AFR) AF: 0.877 AC: 26870 AN: 30645

American (AMR) AF: 0.395 AC: 4157 AN: 10536

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1040 AN: 2636

East Asian (EAS) AF: 0.184 AC: 652 AN: 3549

South Asian (SAS) AF: 0.423 AC: 1133 AN: 2676

European-Finnish (FIN) AF: 0.510 AC: 3011 AN: 5909

Middle Eastern (MID) AF: 0.458 AC: 98 AN: 214

European-Non Finnish (NFE) AF: 0.531 AC: 28149 AN: 52972

Other (OTH) AF: 0.535 AC: 813 AN: 1520

Alfa AF: 0.556 Hom.: 64709

Bravo AF: 0.592

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.3
DANN	Benign	0.32
PhyloP100		1.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9306749; hg19: chrX-14493455;