5-132420366-A-G

Variant names:

• chr5-132420366-A-G
• rs11242111
• ENST00000638452.2:c.-209+426A>G

Variant summary

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

The ENST00000638452.2(ENSG00000283782):​c.-209+426A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.86 in 152,228 control chromosomes in the GnomAD database, including 57,843 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 0.86 (57843 hom., cov: 32)
• Consequence: ENSG00000283782 ENST00000638452.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.34
• Publications: 23 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.958 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CARINH	NR_161242.1	n.231+426A>G		intron_variant	Intron 2 of 3
LINC02863	NR_186386.1	n.430-617T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000283782	ENST00000638452.2	c.-209+426A>G		intron_variant	Intron 2 of 26	5		ENSP00000492349.2

Frequencies

GnomAD3 genomes AF: 0.860 AC: 130787 AN: 152110 Hom.: 57824 Cov.: 32

Gnomad AFR AF: 0.628

Gnomad AMI AF: 0.952

Gnomad AMR AF: 0.915

Gnomad ASJ AF: 0.930

Gnomad EAS AF: 0.981

Gnomad SAS AF: 0.976

Gnomad FIN AF: 0.969

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.949

Gnomad OTH AF: 0.872

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

GnomAD4 genome AF: 0.860 AC: 130854 AN: 152228 Hom.: 57843 Cov.: 32 AF XY: 0.863 AC XY: 64271 AN XY: 74444

African (AFR) AF: 0.627 AC: 26025 AN: 41480

American (AMR) AF: 0.915 AC: 13999 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.930 AC: 3228 AN: 3470

East Asian (EAS) AF: 0.981 AC: 5086 AN: 5186

South Asian (SAS) AF: 0.976 AC: 4711 AN: 4828

European-Finnish (FIN) AF: 0.969 AC: 10290 AN: 10622

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.949 AC: 64578 AN: 68018

Other (OTH) AF: 0.872 AC: 1846 AN: 2116

Alfa AF: 0.907 Hom.: 100110

Bravo AF: 0.844

Asia WGS AF: 0.950 AC: 3305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.28
DANN	Benign	0.33
PhyloP100		-2.3

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: rs11242111; hg19: chr5-131756058;