rs2419050

chr1-67857777-A-G

Variant summary

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

The NR_040077.1(GNG12-AS1):n.149+25341A>G 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 0.562 in 151,998 control chromosomes in the GnomAD database, including 24,510 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 0.56 (24510 hom., cov: 32)
• Consequence: GNG12-AS1 NR_040077.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.424

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.668 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GNG12-AS1	NR_040077.1	n.149+25341A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GNG12-AS1	ENST00000420587.5	n.134+25341A>G		intron_variant, non_coding_transcript_variant		2
GNG12-AS1	ENST00000413628.5	n.128+25341A>G		intron_variant, non_coding_transcript_variant		2
GNG12-AS1	ENST00000688125.2	n.145-15375A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85382 AN: 151882 Hom.: 24497 Cov.: 32

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.602

Gnomad SAS AF: 0.562

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.562 AC: 85427 AN: 151998 Hom.: 24510 Cov.: 32 AF XY: 0.561 AC XY: 41653 AN XY: 74300

Gnomad4 AFR AF: 0.446

Gnomad4 AMR AF: 0.679

Gnomad4 ASJ AF: 0.699

Gnomad4 EAS AF: 0.602

Gnomad4 SAS AF: 0.563

Gnomad4 FIN AF: 0.475

Gnomad4 NFE AF: 0.609

Gnomad4 OTH AF: 0.602

Alfa AF: 0.584 Hom.: 5322

Bravo AF: 0.572

Asia WGS AF: 0.563 AC: 1957 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	4.0
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2419050; hg19: chr1-68323460;