rs2352162

chr8-111564236-T-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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02237	ENST00000524236.2	n.481+21252T>C		intron_variant, non_coding_transcript_variant		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;