rs2106854

chr5-132433482-C-T

Variant summary

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

The XR_007058935.1(LOC124901064):n.7267G>A 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 0.23 in 151,712 control chromosomes in the GnomAD database, including 4,200 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 0.23 (4200 hom., cov: 32)
• Consequence: LOC124901064 XR_007058935.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.304

Genes affected

LOC124901064 (HGNC:):

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=-0.6).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901064	XR_007058935.1	n.7267G>A		non_coding_transcript_exon_variant	2/2
IRF1-AS1	NR_161242.1	n.231+13542C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IRF1-AS1	ENST00000612967.2	n.240+13542C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34910 AN: 151594 Hom.: 4202 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.0639

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.230 AC: 34924 AN: 151712 Hom.: 4200 Cov.: 32 AF XY: 0.235 AC XY: 17453 AN XY: 74128

Gnomad4 AFR AF: 0.246

Gnomad4 AMR AF: 0.193

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.355

Gnomad4 SAS AF: 0.397

Gnomad4 FIN AF: 0.226

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.230

Alfa AF: 0.226 Hom.: 609

Bravo AF: 0.224

Asia WGS AF: 0.371 AC: 1288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
Cadd	Benign	15
Dann	Benign	0.80

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: rs2106854; hg19: chr5-131769174;