chr3-160001345-A-G

Position:

• chr3-160001345-A-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.823-3240T>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 0.56 in 151,954 control chromosomes in the GnomAD database, including 25,659 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 0.56 (25659 hom., cov: 32)
• Consequence: IL12A-AS1 NR_108088.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.312

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.787 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL12A-AS1	NR_108088.1	n.823-3240T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL12A-AS1	ENST00000497452.5	n.823-3240T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.560 AC: 84967 AN: 151836 Hom.: 25614 Cov.: 32

Gnomad AFR AF: 0.794

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.529

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.560 AC: 85071 AN: 151954 Hom.: 25659 Cov.: 32 AF XY: 0.550 AC XY: 40839 AN XY: 74240

Gnomad4 AFR AF: 0.794

Gnomad4 AMR AF: 0.402

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.502

Gnomad4 FIN AF: 0.452

Gnomad4 NFE AF: 0.509

Gnomad4 OTH AF: 0.504

Alfa AF: 0.506 Hom.: 26454

Bravo AF: 0.562

Asia WGS AF: 0.442 AC: 1538 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.5
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs485497; hg19: chr3-159719132;