chrX-14534951-C-T

Position:

• chrX-14534951-C-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_002063.4(GLRA2):​c.202+2579C>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 0.57 (13785 hom., 17772 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: GLRA2 NM_002063.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0700

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 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GLRA2	NM_002063.4	c.202+2579C>T		intron_variant		ENST00000218075.9	NP_002054.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GLRA2	ENST00000218075.9	c.202+2579C>T		intron_variant		1	NM_002063.4	ENSP00000218075.4
GLRA2	ENST00000355020.9	c.202+2579C>T		intron_variant		1		ENSP00000347123.4
GLRA2	ENST00000415367.2	n.453+2579C>T		intron_variant		3
GLRA2	ENST00000443437.6	n.*169+2579C>T		intron_variant		2		ENSP00000387756.3

Frequencies

GnomAD3 genomes AF: 0.570 AC: 62377 AN: 109495 Hom.: 13785 Cov.: 22 AF XY: 0.554 AC XY: 17724 AN XY: 31973

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.467

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.520

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: 0.570 AC: 62424 AN: 109549 Hom.: 13785 Cov.: 22 AF XY: 0.555 AC XY: 17772 AN XY: 32037

Gnomad4 AFR AF: 0.777

Gnomad4 AMR AF: 0.375

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.422

Gnomad4 FIN AF: 0.511

Gnomad4 NFE AF: 0.538

Gnomad4 OTH AF: 0.516

Alfa AF: 0.513 Hom.: 12636

Bravo AF: 0.561

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.95
DANN	Benign	0.40

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: rs3027322; hg19: chrX-14553073;