rs725667

chr1-68022967-C-T

Variant summary

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

The NR_040077.1(GNG12-AS1):n.150-11680C>T 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 0.2 in 152,016 control chromosomes in the GnomAD database, including 8,488 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 0.20 (8488 hom., cov: 32)
• Consequence: GNG12-AS1 NR_040077.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.984

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.623 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GNG12-AS1	NR_040077.1	n.150-11680C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GNG12-AS1	ENST00000420587.5	n.135-11680C>T		intron_variant, non_coding_transcript_variant		2
GNG12-AS1	ENST00000413628.5	n.236-48833C>T		intron_variant, non_coding_transcript_variant		2
GNG12-AS1	ENST00000414904.1	n.488-1552C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30245 AN: 151898 Hom.: 8445 Cov.: 32

Gnomad AFR AF: 0.628

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.0900

Gnomad ASJ AF: 0.0671

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0131

Gnomad FIN AF: 0.00982

Gnomad MID AF: 0.0860

Gnomad NFE AF: 0.0304

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.200 AC: 30346 AN: 152016 Hom.: 8488 Cov.: 32 AF XY: 0.193 AC XY: 14322 AN XY: 74306

Gnomad4 AFR AF: 0.629

Gnomad4 AMR AF: 0.0897

Gnomad4 ASJ AF: 0.0671

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0133

Gnomad4 FIN AF: 0.00982

Gnomad4 NFE AF: 0.0305

Gnomad4 OTH AF: 0.160

Alfa AF: 0.101 Hom.: 820

Bravo AF: 0.226

Asia WGS AF: 0.0560 AC: 195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.69
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs725667; hg19: chr1-68488650;