rs5934186

chrX-14660373-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002063.4(GLRA2):c.931-30337A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 110,793 control chromosomes in the GnomAD database, including 1,760 homozygotes. There are 6,459 hemizygotes in GnomAD. 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 0.20 (1760 hom., 6459 hem., cov: 22)
• Consequence: GLRA2 NM_002063.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.279

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.24 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GLRA2	NM_002063.4	c.931-30337A>C		intron_variant		ENST00000218075.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GLRA2	ENST00000218075.9	c.931-30337A>C		intron_variant		1	NM_002063.4	A1
GLRA2	ENST00000355020.9	c.931-30337A>C		intron_variant		1		P4
GLRA2	ENST00000443437.6	c.*858-30337A>C		intron_variant, NMD_transcript_variant		2
GLRA2	ENST00000415367.2	n.1182-30337A>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.201 AC: 22258 AN: 110739 Hom.: 1760 Cov.: 22 AF XY: 0.195 AC XY: 6457 AN XY: 33033

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.539

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.0785

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.201 AC: 22253 AN: 110793 Hom.: 1760 Cov.: 22 AF XY: 0.195 AC XY: 6459 AN XY: 33097

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.233

Gnomad4 EAS AF: 0.0788

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.246

Gnomad4 NFE AF: 0.243

Gnomad4 OTH AF: 0.193

Alfa AF: 0.227 Hom.: 12468

Bravo AF: 0.191

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.68
Dann	Benign	0.51

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs5934186; hg19: chrX-14678495;