chr3-159926508-A-G

Variant summary

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

The NR_108088.1(IL12A-AS1):​n.1351-12034T>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 0.177 in 152,174 control chromosomes in the GnomAD database, including 2,636 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 0.18 ( 2636 hom., cov: 32)

Consequence

IL12A-AS1
NR_108088.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.263
Variant links:
Genes affected
IL12A-AS1 (HGNC:49094): (IL12A 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=-0.86).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
IL12A-AS1NR_108088.1 linkuse as main transcriptn.1351-12034T>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IL12A-AS1ENST00000497452.5 linkuse as main transcriptn.1351-12034T>C intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.177
AC:
26970
AN:
152056
Hom.:
2634
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.106
Gnomad AMI
AF:
0.234
Gnomad AMR
AF:
0.191
Gnomad ASJ
AF:
0.172
Gnomad EAS
AF:
0.0887
Gnomad SAS
AF:
0.350
Gnomad FIN
AF:
0.160
Gnomad MID
AF:
0.209
Gnomad NFE
AF:
0.214
Gnomad OTH
AF:
0.182
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.177
AC:
26992
AN:
152174
Hom.:
2636
Cov.:
32
AF XY:
0.178
AC XY:
13238
AN XY:
74396
show subpopulations
Gnomad4 AFR
AF:
0.106
Gnomad4 AMR
AF:
0.191
Gnomad4 ASJ
AF:
0.172
Gnomad4 EAS
AF:
0.0891
Gnomad4 SAS
AF:
0.349
Gnomad4 FIN
AF:
0.160
Gnomad4 NFE
AF:
0.214
Gnomad4 OTH
AF:
0.184
Alfa
AF:
0.209
Hom.:
4699
Bravo
AF:
0.172
Asia WGS
AF:
0.223
AC:
777
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
7.7
DANN
Benign
0.76

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: rs6799788; hg19: chr3-159644297; API