dbSNP rs4712029: GCLC-AS1:n.111-2747A>G (chr6-53452214-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000789578.1(GCLC-AS1):n.111-2747A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 152,054 control chromosomes in the GnomAD database, including 5,920 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 0.25 ( 5920 hom., cov: 32)

Consequence

GCLC-AS1
ENST00000789578.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.141

Publications

3 publications found

Variant links:

Genes affected

GCLC-AS1 (HGNC:56649): (GCLC antisense RNA 1)

GCLC-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GCLC-AS1	NR_183318.1 link	n.147-2747A>G		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GCLC-AS1	ENST00000789578.1 link	n.111-2747A>G		intron_variant	Intron 1 of 4
GCLC-AS1	ENST00000789579.1 link	n.92-2747A>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.255

AC:

38685

AN:

151938

Hom.:

5917

Cov.:

show subpopulations

Gnomad AFR

AF:

0.139

Gnomad AMI

AF:

0.167

Gnomad AMR

AF:

0.368

Gnomad ASJ

AF:

0.171

Gnomad EAS

AF:

0.563

Gnomad SAS

AF:

0.354

Gnomad FIN

AF:

0.429

Gnomad MID

AF:

0.207

Gnomad NFE

AF:

0.248

Gnomad OTH

AF:

0.236

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

GnomAD4 genome

AF:

0.254

AC:

38687

AN:

152054

Hom.:

5920

Cov.:

AF XY:

0.269

AC XY:

19970

AN XY:

74324

show subpopulations

African (AFR)

AF:

0.139

AC:

5755

AN:

41526

American (AMR)

AF:

0.369

AC:

5630

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.171

AC:

593

AN:

3470

East Asian (EAS)

AF:

0.563

AC:

2903

AN:

5156

South Asian (SAS)

AF:

0.352

AC:

1696

AN:

4812

European-Finnish (FIN)

AF:

0.429

AC:

4526

AN:

10562

Middle Eastern (MID)

AF:

0.209

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.248

AC:

16870

AN:

67944

Other (OTH)

AF:

0.237

AC:

501

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1360

2720

4079

5439

6799

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

402

804

1206

1608

2010

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.248

Hom.:

13391

Bravo

AF:

0.246

Asia WGS

AF:

0.442

AC:

1534

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.92

(source)

DANN

Benign

0.36

PhyloP100

0.14

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over