X-14534951-C-T

Variant names:

• chrX-14534951-C-T
• rs3027322
• NM_002063.4:c.202+2579C>T

Variant summary

Our verdict is Likely benign. The variant received -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
• Publications: 1 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=-0.95).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GLRA2	NM_002063.4	c.202+2579C>T		intron_variant	Intron 2 of 8	ENST00000218075.9	NP_002054.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GLRA2	ENST00000218075.9	c.202+2579C>T		intron_variant	Intron 2 of 8	1	NM_002063.4	ENSP00000218075.4
GLRA2	ENST00000355020.9	c.202+2579C>T		intron_variant	Intron 2 of 8	1		ENSP00000347123.4
GLRA2	ENST00000415367.2	n.453+2579C>T		intron_variant	Intron 2 of 8	3
GLRA2	ENST00000443437.6	n.*169+2579C>T		intron_variant	Intron 4 of 10	2		ENSP00000387756.3

Frequencies

GnomAD3 genomes AF: 0.570 AC: 62377 AN: 109495 Hom.: 13785 Cov.: 22

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

African (AFR) AF: 0.777 AC: 23543 AN: 30299

American (AMR) AF: 0.375 AC: 3847 AN: 10252

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1036 AN: 2603

East Asian (EAS) AF: 0.179 AC: 620 AN: 3466

South Asian (SAS) AF: 0.422 AC: 1103 AN: 2616

European-Finnish (FIN) AF: 0.511 AC: 2936 AN: 5743

Middle Eastern (MID) AF: 0.466 AC: 97 AN: 208

European-Non Finnish (NFE) AF: 0.538 AC: 28061 AN: 52195

Other (OTH) AF: 0.516 AC: 774 AN: 1500

Alfa AF: 0.529 Hom.: 19786

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
PhyloP100		0.070
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3027322; hg19: chrX-14553073;