rs12069862

Positions:

• chr1-68026312-G-A

Variant summary

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

The NR_040077.1(GNG12-AS1):​n.150-8335G>A 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 0.135 in 151,962 control chromosomes in the GnomAD database, including 3,301 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 0.14 (3301 hom., cov: 32)
• Consequence: GNG12-AS1 NR_040077.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.78

Genes affected

GNG12-AS1 (HGNC:43938): (GNG12, DIRAS3 and WLS antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GNG12-AS1	NR_040077.1	n.150-8335G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GNG12-AS1	ENST00000420587.5	n.135-8335G>A		intron_variant, non_coding_transcript_variant		2
GNG12-AS1	ENST00000413628.5	n.236-45488G>A		intron_variant, non_coding_transcript_variant		2
GNG12-AS1	ENST00000414904.1	n.608-262G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20531 AN: 151844 Hom.: 3293 Cov.: 32

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.0757

Gnomad ASJ AF: 0.0578

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0188

Gnomad FIN AF: 0.0163

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0378

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.135 AC: 20577 AN: 151962 Hom.: 3301 Cov.: 32 AF XY: 0.132 AC XY: 9808 AN XY: 74292

Gnomad4 AFR AF: 0.387

Gnomad4 AMR AF: 0.0756

Gnomad4 ASJ AF: 0.0578

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.0186

Gnomad4 FIN AF: 0.0163

Gnomad4 NFE AF: 0.0379

Gnomad4 OTH AF: 0.122

Alfa AF: 0.0755 Hom.: 669

Bravo AF: 0.150

Asia WGS AF: 0.0370 AC: 129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.17
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12069862; hg19: chr1-68491995;