rs662959

Variant names:

• chr3-159983443-G-A
• rs662959
• ENST00000497452.5:n.1350+5654C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000497452.5(IL12A-AS1):​n.1350+5654C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 152,118 control chromosomes in the GnomAD database, including 2,050 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 0.16 (2050 hom., cov: 32)
• Consequence: IL12A-AS1 ENST00000497452.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67
• Publications: 19 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL12A-AS1	NR_108088.1	n.1350+5654C>T		intron_variant	Intron 9 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL12A-AS1	ENST00000497452.5	n.1350+5654C>T		intron_variant	Intron 9 of 9	2
IL12A-AS1	ENST00000642756.1	n.778+5654C>T		intron_variant	Intron 4 of 4
IL12A-AS1	ENST00000654530.1	n.837+5654C>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23720 AN: 152000 Hom.: 2050 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.0890

Gnomad AMR AF: 0.0874

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.156 AC: 23756 AN: 152118 Hom.: 2050 Cov.: 32 AF XY: 0.158 AC XY: 11766 AN XY: 74352

African (AFR) AF: 0.194 AC: 8041 AN: 41502

American (AMR) AF: 0.0872 AC: 1334 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 374 AN: 3468

East Asian (EAS) AF: 0.123 AC: 638 AN: 5176

South Asian (SAS) AF: 0.325 AC: 1563 AN: 4816

European-Finnish (FIN) AF: 0.148 AC: 1563 AN: 10566

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.145 AC: 9837 AN: 67982

Other (OTH) AF: 0.130 AC: 274 AN: 2114

Alfa AF: 0.142 Hom.: 2747

Bravo AF: 0.145

Asia WGS AF: 0.252 AC: 876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.13
DANN	Benign	0.39
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs662959; hg19: chr3-159701231;