rs17468244

Positions:

• chr5-125513213-A-G

Variant summary

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

The NR_109887.1(LINC02240):​n.257-6315A>G 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 0.0895 in 152,128 control chromosomes in the GnomAD database, including 766 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 0.090 (766 hom., cov: 32)
• Consequence: LINC02240 NR_109887.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02240	NR_109887.1	n.257-6315A>G		intron_variant, non_coding_transcript_variant
LOC124901056	XR_007058919.1	n.2258-31488T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02240	ENST00000647105.1	n.481-6315A>G		intron_variant, non_coding_transcript_variant
	ENST00000651821.1	n.257-6315A>G		intron_variant, non_coding_transcript_variant
	ENST00000651847.1	n.1077-86453T>C		intron_variant, non_coding_transcript_variant
LINC02240	ENST00000564199.1	n.257-6315A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0895 AC: 13601 AN: 152010 Hom.: 761 Cov.: 32

Gnomad AFR AF: 0.0210

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.0988

Gnomad ASJ AF: 0.0822

Gnomad EAS AF: 0.0696

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.0871

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

GnomAD4 genome AF: 0.0895 AC: 13620 AN: 152128 Hom.: 766 Cov.: 32 AF XY: 0.0905 AC XY: 6732 AN XY: 74360

Gnomad4 AFR AF: 0.0210

Gnomad4 AMR AF: 0.0996

Gnomad4 ASJ AF: 0.0822

Gnomad4 EAS AF: 0.0694

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.0871

Alfa AF: 0.114 Hom.: 874

Bravo AF: 0.0846

Asia WGS AF: 0.103 AC: 356 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.9
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17468244; hg19: chr5-124848906;