rs6862844

Variant names:

• chr5-125030274-A-C
• rs6862844
• ENST00000642715.2:n.520-11883A>C

Variant summary

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

The ENST00000642715.2(LINC02240):​n.520-11883A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.069 in 152,246 control chromosomes in the GnomAD database, including 1,101 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 0.069 (1101 hom., cov: 32)
• Consequence: LINC02240 ENST00000642715.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.939
• Publications: 6 publications found

Genes affected

LINC02240 (HGNC:53118): (long intergenic non-protein coding RNA 2240)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.22 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
LINC02240	ENST00000642715.2	n.520-11883A>C		intron_variant	Intron 2 of 3
LINC02240	ENST00000647105.1	n.205-11883A>C		intron_variant	Intron 1 of 6
LINC02240	ENST00000671535.1	n.620-11883A>C		intron_variant	Intron 3 of 4
LINC02240	ENST00000825653.1	n.349+27261A>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0688 AC: 10469 AN: 152128 Hom.: 1096 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0339

Gnomad ASJ AF: 0.0216

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0304

Gnomad FIN AF: 0.00264

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.00484

Gnomad OTH AF: 0.0489

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

GnomAD4 genome AF: 0.0690 AC: 10508 AN: 152246 Hom.: 1101 Cov.: 32 AF XY: 0.0668 AC XY: 4976 AN XY: 74448

African (AFR) AF: 0.224 AC: 9289 AN: 41510

American (AMR) AF: 0.0338 AC: 517 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0216 AC: 75 AN: 3470

East Asian (EAS) AF: 0.000771 AC: 4 AN: 5188

South Asian (SAS) AF: 0.0305 AC: 147 AN: 4824

European-Finnish (FIN) AF: 0.00264 AC: 28 AN: 10620

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.00484 AC: 329 AN: 68028

Other (OTH) AF: 0.0479 AC: 101 AN: 2110

Alfa AF: 0.0345 Hom.: 523

Bravo AF: 0.0782

Asia WGS AF: 0.0400 AC: 140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.55
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs6862844; hg19: chr5-124365967;