Genetic Variant GCLC-AS1:n.111-13805C>T (chr6-53441156-C-T) – 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.111-13805C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0978 in 152,254 control chromosomes in the GnomAD database, including 855 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 0.098 ( 855 hom., cov: 33)

Consequence

GCLC-AS1
ENST00000789578.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.54

Publications

2 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=-0.92).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GCLC-AS1	NR_183318.1 link	n.146+9517C>T		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.111-13805C>T		intron_variant	Intron 1 of 4
GCLC-AS1	ENST00000789579.1 link	n.91+9517C>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.0978

AC:

14878

AN:

152136

Hom.:

853

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0242

Gnomad AMI

AF:

0.106

Gnomad AMR

AF:

0.111

Gnomad ASJ

AF:

0.119

Gnomad EAS

AF:

0.114

Gnomad SAS

AF:

0.133

Gnomad FIN

AF:

0.131

Gnomad MID

AF:

0.114

Gnomad NFE

AF:

0.129

Gnomad OTH

AF:

0.0946

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

GnomAD4 genome

AF:

0.0978

AC:

14886

AN:

152254

Hom.:

855

Cov.:

AF XY:

0.0997

AC XY:

7418

AN XY:

74436

show subpopulations

African (AFR)

AF:

0.0241

AC:

1003

AN:

41558

American (AMR)

AF:

0.112

AC:

1709

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.119

AC:

413

AN:

3472

East Asian (EAS)

AF:

0.114

AC:

593

AN:

5182

South Asian (SAS)

AF:

0.134

AC:

645

AN:

4824

European-Finnish (FIN)

AF:

0.131

AC:

1390

AN:

10590

Middle Eastern (MID)

AF:

0.112

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.129

AC:

8800

AN:

68016

Other (OTH)

AF:

0.0959

AC:

203

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

705

1410

2115

2820

3525

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

174

348

522

696

870

<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:

0.109

Hom.:

551

Bravo

AF:

0.0920

Asia WGS

AF:

0.115

AC:

401

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.52

(source)

DANN

Benign

0.35

PhyloP100

-2.5

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