rs2285673

Positions:

• chr5-132420277-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_161242.1(IRF1-AS1):​n.231+337C>T 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 0.196 in 152,058 control chromosomes in the GnomAD database, including 3,614 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 0.20 (3614 hom., cov: 32)
• Consequence: IRF1-AS1 NR_161242.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.429

Genes affected

LINC02863 (HGNC:41290): (long intergenic non-protein coding RNA 2863)

IRF1-AS1 (HGNC:33838): (colitis associated IRF1 antisense regulator of intestinal homeostasis)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IRF1-AS1	NR_161242.1	n.231+337C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02863	ENST00000454380.1	n.434-528G>A		intron_variant, non_coding_transcript_variant		3
IRF1-AS1	ENST00000612967.2	n.240+337C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29773 AN: 151940 Hom.: 3609 Cov.: 32

Gnomad AFR AF: 0.0762

Gnomad AMI AF: 0.199

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.196 AC: 29797 AN: 152058 Hom.: 3614 Cov.: 32 AF XY: 0.202 AC XY: 15007 AN XY: 74294

Gnomad4 AFR AF: 0.0763

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.323

Gnomad4 FIN AF: 0.340

Gnomad4 NFE AF: 0.245

Gnomad4 OTH AF: 0.174

Alfa AF: 0.187 Hom.: 1321

Bravo AF: 0.174

Asia WGS AF: 0.263 AC: 917 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.9
DANN	Benign	0.42

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2285673; hg19: chr5-131755969;