5-132435113-C-T

Position:

• chr5-132435113-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.5636G>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 0.282 in 152,136 control chromosomes in the GnomAD database, including 7,798 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 0.28 (7798 hom., cov: 31)
• Consequence: LOC124901064 XR_007058935.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43

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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124901064	XR_007058935.1	n.5636G>A		non_coding_transcript_exon_variant	2/2
IRF1-AS1	NR_161242.1	n.232-14537C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IRF1-AS1	ENST00000612967.2	n.241-14537C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42919 AN: 152018 Hom.: 7801 Cov.: 31

Gnomad AFR AF: 0.0917

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.282 AC: 42910 AN: 152136 Hom.: 7798 Cov.: 31 AF XY: 0.272 AC XY: 20192 AN XY: 74372

Gnomad4 AFR AF: 0.0915

Gnomad4 AMR AF: 0.297

Gnomad4 ASJ AF: 0.410

Gnomad4 EAS AF: 0.00270

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.412

Gnomad4 OTH AF: 0.329

Alfa AF: 0.385 Hom.: 26114

Bravo AF: 0.277

Asia WGS AF: 0.0600 AC: 208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.77
DANN	Benign	0.50

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: rs2188962; hg19: chr5-131770805;