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. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047449425.1(LOC124906252):​c.140-135C>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: LOC124906252 XM_047449425.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.125

Genes affected

LOC124906252 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

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

Gnomad4 AFR AF: 0.396

Gnomad4 AMR AF: 0.309

Gnomad4 ASJ AF: 0.247

Gnomad4 EAS AF: 0.248

Gnomad4 SAS AF: 0.344

Gnomad4 FIN AF: 0.342

Gnomad4 NFE AF: 0.306

Gnomad4 OTH AF: 0.317

Alfa AF: 0.295 Hom.: 10508

Bravo AF: 0.323

Asia WGS AF: 0.324 AC: 1126 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	11
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1075498; hg19: chr3-159756451;