rs699032

chr12-24998193-T-Cchr12-24998193-T-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000549262.6(LINC02909):n.138-602A>G 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 0.145 in 152,184 control chromosomes in the GnomAD database, including 1,797 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 0.15 (1797 hom., cov: 32)
• Consequence: LINC02909 ENST00000549262.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0120

Genes affected

LINC02909 (HGNC:27282): (long intergenic non-protein coding RNA 2909)

IRAG2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IRAG2	NM_001394803.1	c.-35+575T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02909	ENST00000549262.6	n.138-602A>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22068 AN: 152066 Hom.: 1796 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.145 AC: 22081 AN: 152184 Hom.: 1797 Cov.: 32 AF XY: 0.140 AC XY: 10404 AN XY: 74416

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.00231

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.130

Gnomad4 NFE AF: 0.188

Gnomad4 OTH AF: 0.144

Alfa AF: 0.171 Hom.: 2324

Bravo AF: 0.142

Asia WGS AF: 0.0680 AC: 236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
Cadd	Benign	15
Dann	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs699032; hg19: chr12-25151127;