rs6862844

chr5-125030274-A-C

Variant summary

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

The ENST00000647105.1(LINC02240):n.205-11883A>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 0.069 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 ENST00000647105.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.939

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02240	ENST00000647105.1	n.205-11883A>C		intron_variant, non_coding_transcript_variant
LINC02240	ENST00000642715.1	n.520-11883A>C		intron_variant, non_coding_transcript_variant
LINC02240	ENST00000671535.1	n.620-11883A>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.0338

Gnomad4 ASJ AF: 0.0216

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.0305

Gnomad4 FIN AF: 0.00264

Gnomad4 NFE AF: 0.00484

Gnomad4 OTH AF: 0.0479

Alfa AF: 0.0181 Hom.: 96

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6862844; hg19: chr5-124365967;