5-132420366-A-G

Position:

• chr5-132420366-A-G

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+426A>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 0.86 in 152,228 control chromosomes in the GnomAD database, including 57,843 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 0.86 (57843 hom., cov: 32)
• Consequence: IRF1-AS1 NR_161242.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.34

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.958 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IRF1-AS1	NR_161242.1	n.231+426A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02863	ENST00000454380.1	n.434-617T>C		intron_variant, non_coding_transcript_variant		3
IRF1-AS1	ENST00000612967.2	n.240+426A>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.860 AC: 130787 AN: 152110 Hom.: 57824 Cov.: 32

Gnomad AFR AF: 0.628

Gnomad AMI AF: 0.952

Gnomad AMR AF: 0.915

Gnomad ASJ AF: 0.930

Gnomad EAS AF: 0.981

Gnomad SAS AF: 0.976

Gnomad FIN AF: 0.969

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.949

Gnomad OTH AF: 0.872

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

GnomAD4 genome AF: 0.860 AC: 130854 AN: 152228 Hom.: 57843 Cov.: 32 AF XY: 0.863 AC XY: 64271 AN XY: 74444

Gnomad4 AFR AF: 0.627

Gnomad4 AMR AF: 0.915

Gnomad4 ASJ AF: 0.930

Gnomad4 EAS AF: 0.981

Gnomad4 SAS AF: 0.976

Gnomad4 FIN AF: 0.969

Gnomad4 NFE AF: 0.949

Gnomad4 OTH AF: 0.872

Alfa AF: 0.895 Hom.: 5991

Bravo AF: 0.844

Asia WGS AF: 0.950 AC: 3305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.28
DANN	Benign	0.33

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: rs11242111; hg19: chr5-131756058;