rs2285673

Variant names:

• chr5-132420277-C-T
• rs2285673
• ENST00000638452.2:c.-209+337C>T

Variant summary

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

The ENST00000638452.2(ENSG00000283782):​c.-209+337C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 152,058 control chromosomes in the GnomAD database, including 3,614 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 0.20 (3614 hom., cov: 32)
• Consequence: ENSG00000283782 ENST00000638452.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.429
• Publications: 16 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000638452.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CARINH	NR_161242.1		n.231+337C>T		intron	N/A
	LINC02863	NR_186386.1		n.430-528G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000283782	ENST00000638452.2	TSL:5	c.-209+337C>T		intron	N/A	ENSP00000492349.2	A0A1W2PQ90
	CARINH	ENST00000612967.2	TSL:1	n.240+337C>T		intron	N/A
	ENSG00000283782	ENST00000638568.2	TSL:5	c.-351+337C>T		intron	N/A	ENSP00000491158.2	A0A1W2PQ90

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29773 AN: 151940 Hom.: 3609 Cov.: 32

Gnomad AFR AF: 0.0762

Gnomad AMI AF: 0.199

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.196 AC: 29797 AN: 152058 Hom.: 3614 Cov.: 32 AF XY: 0.202 AC XY: 15007 AN XY: 74294

African (AFR) AF: 0.0763 AC: 3165 AN: 41508

American (AMR) AF: 0.215 AC: 3285 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 351 AN: 3468

East Asian (EAS) AF: 0.113 AC: 585 AN: 5158

South Asian (SAS) AF: 0.323 AC: 1554 AN: 4814

European-Finnish (FIN) AF: 0.340 AC: 3592 AN: 10550

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.245 AC: 16669 AN: 67960

Other (OTH) AF: 0.174 AC: 368 AN: 2110

Alfa AF: 0.194 Hom.: 2383

Bravo AF: 0.174

Asia WGS AF: 0.263 AC: 917 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.9
DANN	Benign	0.42
PhyloP100		-0.43

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2285673;

hg19: chr5-131755969;