Variant X-14616743-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002063.4(GLRA2):c.930+7538C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 111,151 control chromosomes in the GnomAD database, including 2,487 homozygotes. There are 7,925 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 0.24 ( 2487 hom., 7925 hem., cov: 23)

Consequence

GLRA2
NM_002063.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.763

Variant links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.99).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GLRA2	NM_002063.4 linkuse as main transcript	c.930+7538C>T		intron_variant		ENST00000218075.9

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
GLRA2	ENST00000218075.9 linkuse as main transcript	c.930+7538C>T	intron_variant	1	NM_002063.4	A1	P23416-1
GLRA2	ENST00000355020.9 linkuse as main transcript	c.930+7538C>T	intron_variant	1		P4	P23416-2
GLRA2	ENST00000443437.6 linkuse as main transcript	c.*857+7538C>T	intron_variant, NMD_transcript_variant	2			P23416-3
GLRA2	ENST00000415367.2 linkuse as main transcript	n.1181+7538C>T	intron_variant, non_coding_transcript_variant	3

Frequencies

GnomAD3 genomes

AF:

0.242

AC:

26939

AN:

111098

Hom.:

2487

Cov.:

AF XY:

0.237

AC XY:

7916

AN XY:

33426

show subpopulations

Gnomad AFR

AF:

0.178

Gnomad AMI

AF:

0.313

Gnomad AMR

AF:

0.193

Gnomad ASJ

AF:

0.215

Gnomad EAS

AF:

0.0113

Gnomad SAS

AF:

0.239

Gnomad FIN

AF:

0.304

Gnomad MID

AF:

0.233

Gnomad NFE

AF:

0.300

Gnomad OTH

AF:

0.224

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

GnomAD4 genome

AF:

0.242

AC:

26948

AN:

111151

Hom.:

2487

Cov.:

AF XY:

0.237

AC XY:

7925

AN XY:

33489

show subpopulations

Gnomad4 AFR

AF:

0.178

Gnomad4 AMR

AF:

0.192

Gnomad4 ASJ

AF:

0.215

Gnomad4 EAS

AF:

0.0113

Gnomad4 SAS

AF:

0.240

Gnomad4 FIN

AF:

0.304

Gnomad4 NFE

AF:

0.300

Gnomad4 OTH

AF:

0.223

Alfa

AF:

0.271

Hom.:

4430

Bravo

AF:

0.229

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

6.5

DANN

Benign

0.53

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over