rs1075498

Variant names:

• chr3-160038664-G-A
• rs1075498
• XM_047449425.1:c.140-135C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-160038664-G-A
• chr3-160038664-G-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.518-13130C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.331 in 143,168 control chromosomes in the GnomAD database, including 7,621 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 0.33 (7621 hom., cov: 28)
• Consequence: IL12A-AS1 ENST00000497452.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.125
• Publications: 6 publications found

Genes affected

LOC124906252 (HGNC:):

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000497452.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL12A-AS1	NR_108088.1		n.518-13130C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL12A-AS1	ENST00000497452.5	TSL:2	n.518-13130C>T		intron	N/A
	IL12A-AS1	ENST00000642756.1		n.366+246C>T		intron	N/A
	IL12A-AS1	ENST00000654530.1		n.309+246C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.331 AC: 47333 AN: 143068 Hom.: 7593 Cov.: 28

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.331 AC: 47413 AN: 143168 Hom.: 7621 Cov.: 28 AF XY: 0.331 AC XY: 22881 AN XY: 69202

African (AFR) AF: 0.396 AC: 15537 AN: 39238

American (AMR) AF: 0.309 AC: 4440 AN: 14378

Ashkenazi Jewish (ASJ) AF: 0.247 AC: 834 AN: 3376

East Asian (EAS) AF: 0.248 AC: 1132 AN: 4566

South Asian (SAS) AF: 0.344 AC: 1500 AN: 4362

European-Finnish (FIN) AF: 0.342 AC: 2916 AN: 8528

Middle Eastern (MID) AF: 0.272 AC: 69 AN: 254

European-Non Finnish (NFE) AF: 0.306 AC: 20094 AN: 65600

Other (OTH) AF: 0.317 AC: 630 AN: 1990

Alfa AF: 0.301 Hom.: 25744

Bravo AF: 0.323

Asia WGS AF: 0.324 AC: 1126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	11
DANN	Benign	0.54
PhyloP100		0.13

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1075498;

hg19: chr3-159756451;