ENST00000413628.5:n.235+26716A>G

Variant names:

• chr1-67982978-A-G
• rs1926283
• ENST00000413628.5:n.235+26716A>G

Variant summary

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

The ENST00000413628.5(GNG12-AS1):​n.235+26716A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 152,136 control chromosomes in the GnomAD database, including 4,909 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 0.16 (4909 hom., cov: 32)
• Consequence: GNG12-AS1 ENST00000413628.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76
• 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=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GNG12-AS1	NR_040077.1	n.150-51669A>G		intron_variant	Intron 1 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GNG12-AS1	ENST00000413628.5	n.235+26716A>G		intron_variant	Intron 2 of 8	2
GNG12-AS1	ENST00000414904.1	n.487+26716A>G		intron_variant	Intron 2 of 3	3
GNG12-AS1	ENST00000420587.5	n.135-51669A>G		intron_variant	Intron 1 of 9	2

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24519 AN: 152018 Hom.: 4886 Cov.: 32

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0858

Gnomad ASJ AF: 0.0518

Gnomad EAS AF: 0.0866

Gnomad SAS AF: 0.0612

Gnomad FIN AF: 0.0261

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0291

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.162 AC: 24581 AN: 152136 Hom.: 4909 Cov.: 32 AF XY: 0.160 AC XY: 11932 AN XY: 74398

African (AFR) AF: 0.476 AC: 19744 AN: 41436

American (AMR) AF: 0.0855 AC: 1308 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0518 AC: 180 AN: 3472

East Asian (EAS) AF: 0.0864 AC: 447 AN: 5174

South Asian (SAS) AF: 0.0600 AC: 289 AN: 4816

European-Finnish (FIN) AF: 0.0261 AC: 277 AN: 10610

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.0291 AC: 1981 AN: 68014

Other (OTH) AF: 0.128 AC: 271 AN: 2112

Alfa AF: 0.0449 Hom.: 330

Bravo AF: 0.181

Asia WGS AF: 0.0870 AC: 302 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.39
DANN	Benign	0.53
PhyloP100		-1.8
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: rs1926283; hg19: chr1-68448661;