rs2352163

Variant names:

• chr8-111564449-A-C
• rs2352163
• ENST00000524236.2:n.481+21465A>C

Your query was ambiguous. Multiple possible variants found:

• chr8-111564449-A-C
• chr8-111564449-A-G
• chr8-111564449-A-T

Variant summary

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

The ENST00000524236.2(LINC02237):​n.481+21465A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.908 in 152,044 control chromosomes in the GnomAD database, including 62,788 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 0.91 (62788 hom., cov: 30)
• Consequence: LINC02237 ENST00000524236.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.929
• Publications: 0 publications found

Genes affected

LINC02237 (HGNC:53108): (long intergenic non-protein coding RNA 2237)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.936 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000524236.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02237	ENST00000524236.2	TSL:3	n.481+21465A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.908 AC: 138011 AN: 151926 Hom.: 62750 Cov.: 30

Gnomad AFR AF: 0.944

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.863

Gnomad ASJ AF: 0.846

Gnomad EAS AF: 0.860

Gnomad SAS AF: 0.869

Gnomad FIN AF: 0.901

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.910

Gnomad OTH AF: 0.903

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

GnomAD4 genome AF: 0.908 AC: 138105 AN: 152044 Hom.: 62788 Cov.: 30 AF XY: 0.904 AC XY: 67213 AN XY: 74310

African (AFR) AF: 0.944 AC: 39133 AN: 41462

American (AMR) AF: 0.863 AC: 13159 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.846 AC: 2936 AN: 3472

East Asian (EAS) AF: 0.860 AC: 4419 AN: 5140

South Asian (SAS) AF: 0.869 AC: 4188 AN: 4822

European-Finnish (FIN) AF: 0.901 AC: 9528 AN: 10576

Middle Eastern (MID) AF: 0.918 AC: 270 AN: 294

European-Non Finnish (NFE) AF: 0.910 AC: 61862 AN: 68010

Other (OTH) AF: 0.904 AC: 1903 AN: 2106

Alfa AF: 0.904 Hom.: 20890

Bravo AF: 0.909

Asia WGS AF: 0.858 AC: 2981 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.3
DANN	Benign	0.67
PhyloP100		-0.93

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2352163; hg19: chr8-112576678;