rs2352162

Variant names:

• chr8-111564236-T-C
• rs2352162
• ENST00000524236.2:n.481+21252T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000524236.2(LINC02237):​n.481+21252T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 151,782 control chromosomes in the GnomAD database, including 11,288 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 0.36 (11288 hom., cov: 30)
• Consequence: LINC02237 ENST00000524236.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.231

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02237	ENST00000524236.2	n.481+21252T>C		intron_variant	Intron 5 of 7	3

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54190 AN: 151664 Hom.: 11291 Cov.: 30

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.357 AC: 54187 AN: 151782 Hom.: 11288 Cov.: 30 AF XY: 0.352 AC XY: 26132 AN XY: 74134

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.310

Gnomad4 ASJ AF: 0.416

Gnomad4 EAS AF: 0.156

Gnomad4 SAS AF: 0.312

Gnomad4 FIN AF: 0.451

Gnomad4 NFE AF: 0.488

Gnomad4 OTH AF: 0.388

Alfa AF: 0.403 Hom.: 1692

Bravo AF: 0.340

Asia WGS AF: 0.245 AC: 850 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.8
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2352162; hg19: chr8-112576465;