rs4712029

Positions:

• chr6-53452214-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_183318.1(GCLC-AS1):​n.147-2747A>G variant causes a intron, non coding transcript 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 NR_183318.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.141

Genes affected

GCLC-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
GCLC-AS1	NR_183318.1	n.147-2747A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38685 AN: 151938 Hom.: 5917 Cov.: 32

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.: 32 AF XY: 0.269 AC XY: 19970 AN XY: 74324

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.369

Gnomad4 ASJ AF: 0.171

Gnomad4 EAS AF: 0.563

Gnomad4 SAS AF: 0.352

Gnomad4 FIN AF: 0.429

Gnomad4 NFE AF: 0.248

Gnomad4 OTH AF: 0.237

Alfa AF: 0.250 Hom.: 8044

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
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4712029; hg19: chr6-53317012;