ENST00000564199.1:n.257-6315A>G

Variant names:

• chr5-125513213-A-G
• rs17468244
• ENST00000564199.1:n.257-6315A>G

Variant summary

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

The ENST00000564199.1(LINC02240):​n.257-6315A>G variant causes a intron 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 ENST00000564199.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05
• Publications: 5 publications found

Genes affected

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

ENSG00000248752 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC02240	NR_109887.1	n.257-6315A>G		intron_variant	Intron 2 of 3
LOC124901056	XR_007058919.1	n.2258-31488T>C		intron_variant	Intron 8 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02240	ENST00000564199.1	n.257-6315A>G		intron_variant	Intron 2 of 3	2
LINC02240	ENST00000647105.1	n.481-6315A>G		intron_variant	Intron 4 of 6
ENSG00000248752	ENST00000651847.1	n.1077-86453T>C		intron_variant	Intron 12 of 15

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

African (AFR) AF: 0.0210 AC: 873 AN: 41566

American (AMR) AF: 0.0996 AC: 1521 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0822 AC: 285 AN: 3468

East Asian (EAS) AF: 0.0694 AC: 357 AN: 5144

South Asian (SAS) AF: 0.127 AC: 611 AN: 4830

European-Finnish (FIN) AF: 0.138 AC: 1459 AN: 10596

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8139 AN: 67942

Other (OTH) AF: 0.0871 AC: 184 AN: 2112

Alfa AF: 0.110 Hom.: 2251

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
PhyloP100		1.0
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs17468244; hg19: chr5-124848906;