rs755004

Positions:

• chr3-159982537-G-A
• chr3-159982537-G-C

Variant summary

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

The NR_108088.1(IL12A-AS1):​n.1350+6560C>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 0.106 in 152,234 control chromosomes in the GnomAD database, including 1,025 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 0.11 (1025 hom., cov: 33)
• Consequence: IL12A-AS1 NR_108088.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.205

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL12A-AS1	NR_108088.1	n.1350+6560C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL12A-AS1	ENST00000497452.5	n.1350+6560C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16080 AN: 152116 Hom.: 1021 Cov.: 33

Gnomad AFR AF: 0.0359

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.0790

Gnomad EAS AF: 0.0811

Gnomad SAS AF: 0.0987

Gnomad FIN AF: 0.0955

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.106 AC: 16090 AN: 152234 Hom.: 1025 Cov.: 33 AF XY: 0.104 AC XY: 7748 AN XY: 74420

Gnomad4 AFR AF: 0.0358

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.0790

Gnomad4 EAS AF: 0.0810

Gnomad4 SAS AF: 0.0990

Gnomad4 FIN AF: 0.0955

Gnomad4 NFE AF: 0.145

Gnomad4 OTH AF: 0.110

Alfa AF: 0.131 Hom.: 1928

Bravo AF: 0.108

Asia WGS AF: 0.0720 AC: 252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.4
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs755004; hg19: chr3-159700325;