rs9306749

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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GLRA2	XM_047441999.1	c.-111+26055C>T		intron_variant	Intron 1 of 9		XP_047297955.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;