chr6-53442896-C-T

Variant names:

• chr6-53442896-C-T
• rs9395865
• ENST00000789578.1:n.111-12065C>T

Variant summary

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

The NR_183318.1(GCLC-AS1):​n.146+11257C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.418 in 151,982 control chromosomes in the GnomAD database, including 14,760 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 0.42 (14760 hom., cov: 32)
• Consequence: GCLC-AS1 NR_183318.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.811
• Publications: 5 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_183318.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GCLC-AS1	NR_183318.1		n.146+11257C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GCLC-AS1	ENST00000789578.1		n.111-12065C>T		intron	N/A
	GCLC-AS1	ENST00000789579.1		n.91+11257C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63430 AN: 151862 Hom.: 14745 Cov.: 32

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.309

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.418 AC: 63484 AN: 151982 Hom.: 14760 Cov.: 32 AF XY: 0.430 AC XY: 31932 AN XY: 74280

African (AFR) AF: 0.557 AC: 23097 AN: 41430

American (AMR) AF: 0.507 AC: 7742 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.238 AC: 825 AN: 3468

East Asian (EAS) AF: 0.728 AC: 3767 AN: 5174

South Asian (SAS) AF: 0.394 AC: 1898 AN: 4822

European-Finnish (FIN) AF: 0.462 AC: 4870 AN: 10546

Middle Eastern (MID) AF: 0.315 AC: 92 AN: 292

European-Non Finnish (NFE) AF: 0.297 AC: 20220 AN: 67968

Other (OTH) AF: 0.368 AC: 775 AN: 2108

Alfa AF: 0.338 Hom.: 29621

Bravo AF: 0.432

Asia WGS AF: 0.556 AC: 1929 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.32
DANN	Benign	0.43
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs9395865; hg19: chr6-53307694;