rs17826053

Positions:

• chr3-159999842-T-G

Variant summary

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

The NR_108088.1(IL12A-AS1):​n.823-1737A>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 0.151 in 152,140 control chromosomes in the GnomAD database, including 1,919 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 0.15 (1919 hom., cov: 32)
• Consequence: IL12A-AS1 NR_108088.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0290

Genes affected

IL12A-AS1 (HGNC:49094): (IL12A antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL12A-AS1	NR_108088.1	n.823-1737A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL12A-AS1	ENST00000497452.5	n.823-1737A>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.151 AC: 23015 AN: 152022 Hom.: 1919 Cov.: 32

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.0858

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.151 AC: 23042 AN: 152140 Hom.: 1919 Cov.: 32 AF XY: 0.153 AC XY: 11370 AN XY: 74364

Gnomad4 AFR AF: 0.180

Gnomad4 AMR AF: 0.0857

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.129

Gnomad4 SAS AF: 0.324

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.145

Gnomad4 OTH AF: 0.126

Alfa AF: 0.163 Hom.: 318

Bravo AF: 0.141

Asia WGS AF: 0.245 AC: 849 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.6
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17826053; hg19: chr3-159717629;