chr6-53496891-C-T

Variant names:

• chr6-53496891-C-T
• rs4140528
• ENST00000789578.1:n.291-9437C>T

Variant summary

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

The ENST00000789578.1(GCLC-AS1):​n.291-9437C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 152,010 control chromosomes in the GnomAD database, including 6,209 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 0.28 (6209 hom., cov: 32)
• Consequence: GCLC-AS1 ENST00000789578.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 8 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.361 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.327-9263C>T		intron	N/A
	GCLC-AS1	NR_183319.1		n.127+3255C>T		intron	N/A
	GCLC-AS1	NR_183320.1		n.83+2204C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GCLC-AS1	ENST00000789578.1		n.291-9437C>T		intron	N/A
	GCLC-AS1	ENST00000789579.1		n.269-9269C>T		intron	N/A
	GCLC-AS1	ENST00000789580.1		n.199-9907C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42309 AN: 151892 Hom.: 6202 Cov.: 32

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.279 AC: 42349 AN: 152010 Hom.: 6209 Cov.: 32 AF XY: 0.272 AC XY: 20229 AN XY: 74300

African (AFR) AF: 0.366 AC: 15177 AN: 41446

American (AMR) AF: 0.192 AC: 2929 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 803 AN: 3468

East Asian (EAS) AF: 0.136 AC: 705 AN: 5172

South Asian (SAS) AF: 0.142 AC: 684 AN: 4824

European-Finnish (FIN) AF: 0.275 AC: 2900 AN: 10552

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18314 AN: 67954

Other (OTH) AF: 0.265 AC: 559 AN: 2108

Alfa AF: 0.280 Hom.: 897

Bravo AF: 0.277

Asia WGS AF: 0.146 AC: 507 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.36
DANN	Benign	0.70
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs4140528; hg19: chr6-53361689;