chr1-67982978-A-G

Position:

• chr1-67982978-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.150-51669A>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 0.162 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 NR_040077.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76

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=-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/exons	MANE	Protein	UniProt
GNG12-AS1	NR_040077.1	n.150-51669A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GNG12-AS1	ENST00000420587.5	n.135-51669A>G		intron_variant, non_coding_transcript_variant		2
GNG12-AS1	ENST00000413628.5	n.235+26716A>G		intron_variant, non_coding_transcript_variant		2
GNG12-AS1	ENST00000414904.1	n.487+26716A>G		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.476

Gnomad4 AMR AF: 0.0855

Gnomad4 ASJ AF: 0.0518

Gnomad4 EAS AF: 0.0864

Gnomad4 SAS AF: 0.0600

Gnomad4 FIN AF: 0.0261

Gnomad4 NFE AF: 0.0291

Gnomad4 OTH AF: 0.128

Alfa AF: 0.0450 Hom.: 294

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1926283; hg19: chr1-68448661;