rs2269822

Positions:

• chr5-132423020-T-C
• chr5-132423020-T-G

Variant summary

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

The XR_007058935.1(LOC124901064):​n.17729A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.799 in 152,212 control chromosomes in the GnomAD database, including 49,747 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 0.80 (49747 hom., cov: 33)
• Consequence: LOC124901064 XR_007058935.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.692

Genes affected

LOC124901064 (HGNC:):

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=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.895 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901064	XR_007058935.1	n.17729A>G		non_coding_transcript_exon_variant	2/2
IRF1-AS1	NR_161242.1	n.231+3080T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02863	ENST00000454380.1	n.433+3262A>G		intron_variant, non_coding_transcript_variant		3
IRF1-AS1	ENST00000612967.2	n.240+3080T>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.799 AC: 121576 AN: 152094 Hom.: 49721 Cov.: 33

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.870

Gnomad ASJ AF: 0.824

Gnomad EAS AF: 0.712

Gnomad SAS AF: 0.917

Gnomad FIN AF: 0.897

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.880

Gnomad OTH AF: 0.807

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

GnomAD4 genome AF: 0.799 AC: 121652 AN: 152212 Hom.: 49747 Cov.: 33 AF XY: 0.803 AC XY: 59752 AN XY: 74422

Gnomad4 AFR AF: 0.610

Gnomad4 AMR AF: 0.870

Gnomad4 ASJ AF: 0.824

Gnomad4 EAS AF: 0.713

Gnomad4 SAS AF: 0.917

Gnomad4 FIN AF: 0.897

Gnomad4 NFE AF: 0.880

Gnomad4 OTH AF: 0.808

Alfa AF: 0.803 Hom.: 2675

Bravo AF: 0.787

Asia WGS AF: 0.834 AC: 2899 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	11
DANN	Benign	0.83

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: rs2269822; hg19: chr5-131758712;