rs1439568

Variant names:

• chr5-125210039-T-C
• rs1439568
• ENST00000647105.1:n.288-115313T>C

Variant summary

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

The ENST00000647105.1(LINC02240):​n.288-115313T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 152,122 control chromosomes in the GnomAD database, including 13,016 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 0.41 (13016 hom., cov: 33)
• Consequence: LINC02240 ENST00000647105.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.857
• Publications: 6 publications found

Genes affected

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

LOC101927421 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927421	NR_109882.1	n.377+40413T>C		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02240	ENST00000647105.1	n.288-115313T>C		intron_variant	Intron 2 of 6
LINC02240	ENST00000825646.1	n.278+40413T>C		intron_variant	Intron 4 of 5
LINC02240	ENST00000825648.1	n.276+40413T>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61821 AN: 152004 Hom.: 12999 Cov.: 33

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.0866

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.407 AC: 61879 AN: 152122 Hom.: 13016 Cov.: 33 AF XY: 0.406 AC XY: 30189 AN XY: 74380

African (AFR) AF: 0.408 AC: 16953 AN: 41518

American (AMR) AF: 0.372 AC: 5669 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.368 AC: 1278 AN: 3472

East Asian (EAS) AF: 0.0872 AC: 452 AN: 5186

South Asian (SAS) AF: 0.331 AC: 1595 AN: 4824

European-Finnish (FIN) AF: 0.514 AC: 5439 AN: 10580

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.429 AC: 29147 AN: 67972

Other (OTH) AF: 0.390 AC: 822 AN: 2110

Alfa AF: 0.412 Hom.: 21128

Bravo AF: 0.395

Asia WGS AF: 0.236 AC: 819 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	5.8
DANN	Benign	0.75
PhyloP100		0.86

Splicing

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

Other links and lift over

dbSNP: rs1439568; hg19: chr5-124545732;