3-160038664-G-T

Variant names:

• chr3-160038664-G-T
• rs1075498
• ENST00000497452.5:n.518-13130C>A

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000497452.5(IL12A-AS1):​n.518-13130C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0 (0 hom., cov: 28)
  • Failed GnomAD Quality Control
• Consequence: IL12A-AS1 ENST00000497452.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.125
• Publications: 6 publications found

Genes affected

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

LOC124906252 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL12A-AS1	NR_108088.1	n.518-13130C>A		intron_variant	Intron 3 of 9
LOC124906252	XM_047449425.1	c.140-135C>A		intron_variant	Intron 1 of 2		XP_047305381.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL12A-AS1	ENST00000497452.5	n.518-13130C>A		intron_variant	Intron 3 of 9	2
IL12A-AS1	ENST00000642756.1	n.366+246C>A		intron_variant	Intron 1 of 4
IL12A-AS1	ENST00000654530.1	n.309+246C>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 143260 Hom.: 0 Cov.: 28

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

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

GnomAD4 genome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 143260 Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0 AN XY: 69192

African (AFR) AF: 0.00 AC: 0 AN: 39184

American (AMR) AF: 0.00 AC: 0 AN: 14380

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3380

East Asian (EAS) AF: 0.00 AC: 0 AN: 4588

South Asian (SAS) AF: 0.00 AC: 0 AN: 4376

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8554

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 274

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 65670

Other (OTH) AF: 0.00 AC: 0 AN: 1976

Alfa AF: 0.00 Hom.: 25744

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	9.9
DANN	Benign	0.44
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs1075498; hg19: chr3-159756451;