rs1926289

chr1-68000249-T-C

Variant summary

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

The NR_040077.1(GNG12-AS1):n.150-34398T>C 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 0.283 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 NR_040077.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GNG12-AS1	NR_040077.1	n.150-34398T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GNG12-AS1	ENST00000420587.5	n.135-34398T>C		intron_variant, non_coding_transcript_variant		2
GNG12-AS1	ENST00000413628.5	n.235+43987T>C		intron_variant, non_coding_transcript_variant		2
GNG12-AS1	ENST00000414904.1	n.488-24270T>C		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.0792

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.275

Gnomad4 FIN AF: 0.395

Gnomad4 NFE AF: 0.379

Gnomad4 OTH AF: 0.291

Alfa AF: 0.353 Hom.: 4813

Bravo AF: 0.269

Asia WGS AF: 0.289 AC: 999 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	3.9
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1926289; hg19: chr1-68465932;