chr1-68026312-G-A

Variant names:

• chr1-68026312-G-A
• rs12069862
• ENST00000413628.5:n.236-45488G>A

Variant summary

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

The ENST00000413628.5(GNG12-AS1):​n.236-45488G>A variant causes a intron 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 ENST00000413628.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.78
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
GNG12-AS1	NR_040077.1	n.150-8335G>A		intron_variant	Intron 1 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GNG12-AS1	ENST00000413628.5	n.236-45488G>A		intron_variant	Intron 2 of 8	2
GNG12-AS1	ENST00000414904.1	n.608-262G>A		intron_variant	Intron 3 of 3	3
GNG12-AS1	ENST00000420587.5	n.135-8335G>A		intron_variant	Intron 1 of 9	2

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

African (AFR) AF: 0.387 AC: 16022 AN: 41424

American (AMR) AF: 0.0756 AC: 1151 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.0578 AC: 200 AN: 3462

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5176

South Asian (SAS) AF: 0.0186 AC: 90 AN: 4826

European-Finnish (FIN) AF: 0.0163 AC: 173 AN: 10612

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.0379 AC: 2573 AN: 67924

Other (OTH) AF: 0.122 AC: 258 AN: 2110

Alfa AF: 0.0764 Hom.: 759

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
PhyloP100		-3.8
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs12069862; hg19: chr1-68491995;