rs1491402

Variant names:

• chr4-174775117-T-C
• rs1491402
• NM_006529.4:c.200-8087A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006529.4(GLRA3):​c.200-8087A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.38 in 151,998 control chromosomes in the GnomAD database, including 11,192 homozygotes. 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 0.38 (11192 hom., cov: 33)
• Consequence: GLRA3 NM_006529.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.678
• Publications: 1 publications found

Genes affected

GLRA3 (HGNC:4328): (glycine receptor alpha 3) This gene encodes a member of the ligand-gated ion channel protein family. The encoded protein is a member of the glycine receptor subfamily. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2013]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GLRA3	NM_006529.4	c.200-8087A>G		intron_variant	Intron 2 of 9	ENST00000274093.8	NP_006520.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GLRA3	ENST00000274093.8	c.200-8087A>G		intron_variant	Intron 2 of 9	1	NM_006529.4	ENSP00000274093.3
GLRA3	ENST00000340217.5	c.200-8087A>G		intron_variant	Intron 2 of 8	1		ENSP00000345284.5

Frequencies

GnomAD3 genomes AF: 0.380 AC: 57772 AN: 151878 Hom.: 11186 Cov.: 33

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.380 AC: 57818 AN: 151998 Hom.: 11192 Cov.: 33 AF XY: 0.379 AC XY: 28156 AN XY: 74288

African (AFR) AF: 0.332 AC: 13773 AN: 41490

American (AMR) AF: 0.367 AC: 5609 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1635 AN: 3468

East Asian (EAS) AF: 0.470 AC: 2436 AN: 5180

South Asian (SAS) AF: 0.314 AC: 1514 AN: 4820

European-Finnish (FIN) AF: 0.372 AC: 3924 AN: 10544

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.410 AC: 27816 AN: 67904

Other (OTH) AF: 0.373 AC: 789 AN: 2116

Alfa AF: 0.390 Hom.: 1505

Bravo AF: 0.379

Asia WGS AF: 0.384 AC: 1327 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.2
DANN	Benign	0.58
PhyloP100		-0.68
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: rs1491402; hg19: chr4-175696268;