rs12069862

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_040077.1(GNG12-AS1):​n.150-8335G>A 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 0.135 in 151,962 control chromosomes in the GnomAD database, including 3,301 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 0.14 ( 3301 hom., cov: 32)

Consequence

GNG12-AS1
NR_040077.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.78
Variant links:
Genes affected
GNG12-AS1 (HGNC:43938): (GNG12, DIRAS3 and WLS antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
GNG12-AS1NR_040077.1 linkuse as main transcriptn.150-8335G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
GNG12-AS1ENST00000420587.5 linkuse as main transcriptn.135-8335G>A intron_variant, non_coding_transcript_variant 2
GNG12-AS1ENST00000413628.5 linkuse as main transcriptn.236-45488G>A intron_variant, non_coding_transcript_variant 2
GNG12-AS1ENST00000414904.1 linkuse as main transcriptn.608-262G>A intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.135
AC:
20531
AN:
151844
Hom.:
3293
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.387
Gnomad AMI
AF:
0.0724
Gnomad AMR
AF:
0.0757
Gnomad ASJ
AF:
0.0578
Gnomad EAS
AF:
0.000386
Gnomad SAS
AF:
0.0188
Gnomad FIN
AF:
0.0163
Gnomad MID
AF:
0.123
Gnomad NFE
AF:
0.0378
Gnomad OTH
AF:
0.124
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.135
AC:
20577
AN:
151962
Hom.:
3301
Cov.:
32
AF XY:
0.132
AC XY:
9808
AN XY:
74292
show subpopulations
Gnomad4 AFR
AF:
0.387
Gnomad4 AMR
AF:
0.0756
Gnomad4 ASJ
AF:
0.0578
Gnomad4 EAS
AF:
0.000580
Gnomad4 SAS
AF:
0.0186
Gnomad4 FIN
AF:
0.0163
Gnomad4 NFE
AF:
0.0379
Gnomad4 OTH
AF:
0.122
Alfa
AF:
0.0755
Hom.:
669
Bravo
AF:
0.150
Asia WGS
AF:
0.0370
AC:
129
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
0.17
DANN
Benign
0.62

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs12069862; hg19: chr1-68491995; API