rs2397146

Variant names:

• chr6-53495321-G-A
• rs2397146
• ENST00000789578.1:n.291-11007G>A

Variant summary

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

The ENST00000789578.1(GCLC-AS1):​n.291-11007G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 152,050 control chromosomes in the GnomAD database, including 12,737 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 0.37 (12737 hom., cov: 32)
• Consequence: GCLC-AS1 ENST00000789578.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950
• Publications: 11 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.636 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000789578.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GCLC-AS1	NR_183318.1		n.327-10833G>A		intron	N/A
	GCLC-AS1	NR_183319.1		n.127+1685G>A		intron	N/A
	GCLC-AS1	NR_183320.1		n.83+634G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GCLC-AS1	ENST00000789578.1		n.291-11007G>A		intron	N/A
	GCLC-AS1	ENST00000789579.1		n.269-10839G>A		intron	N/A
	GCLC-AS1	ENST00000789580.1		n.199-11477G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.369 AC: 56121 AN: 151932 Hom.: 12697 Cov.: 32

Gnomad AFR AF: 0.642

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.370 AC: 56217 AN: 152050 Hom.: 12737 Cov.: 32 AF XY: 0.366 AC XY: 27227 AN XY: 74326

African (AFR) AF: 0.643 AC: 26661 AN: 41470

American (AMR) AF: 0.263 AC: 4021 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 788 AN: 3468

East Asian (EAS) AF: 0.242 AC: 1253 AN: 5178

South Asian (SAS) AF: 0.453 AC: 2182 AN: 4812

European-Finnish (FIN) AF: 0.224 AC: 2362 AN: 10562

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.266 AC: 18059 AN: 67984

Other (OTH) AF: 0.329 AC: 691 AN: 2098

Alfa AF: 0.305 Hom.: 23542

Bravo AF: 0.381

Asia WGS AF: 0.434 AC: 1510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.77
DANN	Benign	0.19
PhyloP100		-0.095

Splicing

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

Other links and lift over

dbSNP: rs2397146; hg19: chr6-53360119;