rs2352163

Positions:

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

Variant summary

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

The ENST00000524236.2(LINC02237):​n.481+21465A>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 0.908 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.929

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.936 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+21465A>C		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.944

Gnomad4 AMR AF: 0.863

Gnomad4 ASJ AF: 0.846

Gnomad4 EAS AF: 0.860

Gnomad4 SAS AF: 0.869

Gnomad4 FIN AF: 0.901

Gnomad4 NFE AF: 0.910

Gnomad4 OTH AF: 0.904

Alfa AF: 0.907 Hom.: 10430

Bravo AF: 0.909

Asia WGS AF: 0.858 AC: 2981 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2352163; hg19: chr8-112576678;