rs9306749

chrX-14475333-C-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

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

Genes affected

GLRA2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BS2: High Homozygotes in GnomAd at 15599 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GLRA2	XM_047441999.1	c.-111+26055C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.596 AC: 66288 AN: 111277 Hom.: 15599 Cov.: 24 AF XY: 0.579 AC XY: 19372 AN XY: 33485

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

Gnomad4 AFR AF: 0.877

Gnomad4 AMR AF: 0.395

Gnomad4 ASJ AF: 0.395

Gnomad4 EAS AF: 0.184

Gnomad4 SAS AF: 0.423

Gnomad4 FIN AF: 0.510

Gnomad4 NFE AF: 0.531

Gnomad4 OTH AF: 0.535

Alfa AF: 0.531 Hom.: 44461

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9306749; hg19: chrX-14493455;