chr5-132423020-T-C

Variant names:

• chr5-132423020-T-C
• rs2269822
• ENST00000638452.2:c.-209+3080T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000638452.2(ENSG00000283782):​c.-209+3080T>C variant causes a intron 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: ENSG00000283782 ENST00000638452.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.692
• Publications: 7 publications found

Genes affected

ENSG00000283782 (HGNC:):

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

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC02863	NR_186381.1	n.3022A>G		non_coding_transcript_exon_variant	Exon 2 of 2
LINC02863	NR_186382.1	n.3413A>G		non_coding_transcript_exon_variant	Exon 2 of 2
LINC02863	NR_186383.1	n.2906A>G		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000283782	ENST00000638452.2	c.-209+3080T>C		intron_variant	Intron 2 of 26	5		ENSP00000492349.2

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

African (AFR) AF: 0.610 AC: 25333 AN: 41510

American (AMR) AF: 0.870 AC: 13315 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.824 AC: 2860 AN: 3472

East Asian (EAS) AF: 0.713 AC: 3681 AN: 5162

South Asian (SAS) AF: 0.917 AC: 4425 AN: 4824

European-Finnish (FIN) AF: 0.897 AC: 9522 AN: 10620

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.880 AC: 59836 AN: 68012

Other (OTH) AF: 0.808 AC: 1705 AN: 2110

Alfa AF: 0.784 Hom.: 2821

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
PhyloP100		0.69

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

Other links and lift over

dbSNP: rs2269822; hg19: chr5-131758712;