rs1926289

Variant names:

• chr1-68000249-T-C
• rs1926289
• ENST00000413628.5:n.235+43987T>C

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+43987T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 152,004 control chromosomes in the GnomAD database, including 7,364 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 (7364 hom., cov: 32)
• Consequence: GNG12-AS1 ENST00000413628.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• Publications: 6 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000413628.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GNG12-AS1	NR_040077.1		n.150-34398T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GNG12-AS1	ENST00000413628.5	TSL:2	n.235+43987T>C		intron	N/A
	GNG12-AS1	ENST00000414904.1	TSL:3	n.488-24270T>C		intron	N/A
	GNG12-AS1	ENST00000420587.5	TSL:2	n.135-34398T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.283 AC: 43031 AN: 151886 Hom.: 7356 Cov.: 32

Gnomad AFR AF: 0.0793

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.283 AC: 43048 AN: 152004 Hom.: 7364 Cov.: 32 AF XY: 0.285 AC XY: 21169 AN XY: 74312

African (AFR) AF: 0.0792 AC: 3291 AN: 41534

American (AMR) AF: 0.308 AC: 4703 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1091 AN: 3466

East Asian (EAS) AF: 0.321 AC: 1655 AN: 5152

South Asian (SAS) AF: 0.275 AC: 1328 AN: 4822

European-Finnish (FIN) AF: 0.395 AC: 4148 AN: 10510

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.379 AC: 25762 AN: 67940

Other (OTH) AF: 0.291 AC: 613 AN: 2108

Alfa AF: 0.354 Hom.: 5330

Bravo AF: 0.269

Asia WGS AF: 0.289 AC: 999 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.9
DANN	Benign	0.73
PhyloP100		0.21

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1926289;

hg19: chr1-68465932;