chr5-125561596-T-C

Variant names:

• chr5-125561596-T-C
• rs10519822
• ENST00000564199.1:n.325-39620T>C

Variant summary

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

The ENST00000564199.1(LINC02240):​n.325-39620T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0564 in 152,270 control chromosomes in the GnomAD database, including 483 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 0.056 (483 hom., cov: 32)
• Consequence: LINC02240 ENST00000564199.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.328
• Publications: 1 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02240	NR_109887.1	n.325-39620T>C		intron_variant	Intron 3 of 3
LOC124901056	XR_007058919.1	n.2257+50407A>G		intron_variant	Intron 8 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02240	ENST00000564199.1	n.325-39620T>C		intron_variant	Intron 3 of 3	2
LINC02240	ENST00000647105.1	n.549-21951T>C		intron_variant	Intron 5 of 6
ENSG00000248752	ENST00000651847.1	n.1076+50407A>G		intron_variant	Intron 12 of 15

Frequencies

GnomAD3 genomes AF: 0.0563 AC: 8566 AN: 152152 Hom.: 483 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0536

Gnomad ASJ AF: 0.0118

Gnomad EAS AF: 0.0479

Gnomad SAS AF: 0.0255

Gnomad FIN AF: 0.00838

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0174

Gnomad OTH AF: 0.0358

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

GnomAD4 genome AF: 0.0564 AC: 8587 AN: 152270 Hom.: 483 Cov.: 32 AF XY: 0.0543 AC XY: 4046 AN XY: 74462

African (AFR) AF: 0.144 AC: 5996 AN: 41538

American (AMR) AF: 0.0537 AC: 822 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0118 AC: 41 AN: 3472

East Asian (EAS) AF: 0.0480 AC: 249 AN: 5186

South Asian (SAS) AF: 0.0253 AC: 122 AN: 4822

European-Finnish (FIN) AF: 0.00838 AC: 89 AN: 10620

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0174 AC: 1183 AN: 68016

Other (OTH) AF: 0.0354 AC: 75 AN: 2116

Alfa AF: 0.0116 Hom.: 10

Bravo AF: 0.0638

Asia WGS AF: 0.0410 AC: 143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.2
DANN	Benign	0.74
PhyloP100		-0.33
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: rs10519822; hg19: chr5-124897289;