5-125407574-T-C

Variant names:

• chr5-125407574-T-C
• rs2637496
• ENST00000647105.1:n.384-33025T>C

Variant summary

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

The ENST00000647105.1(LINC02240):​n.384-33025T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.863 in 152,168 control chromosomes in the GnomAD database, including 57,043 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 0.86 (57043 hom., cov: 32)
• Consequence: LINC02240 ENST00000647105.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.118
• Publications: 10 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=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.913 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02240	ENST00000647105.1	n.384-33025T>C		intron_variant	Intron 3 of 6
ENSG00000248752	ENST00000651847.1	n.1291+5537A>G		intron_variant	Intron 15 of 15
ENSG00000248752	ENST00000655986.1	n.142+5537A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.863 AC: 131198 AN: 152050 Hom.: 57000 Cov.: 32

Gnomad AFR AF: 0.768

Gnomad AMI AF: 0.898

Gnomad AMR AF: 0.819

Gnomad ASJ AF: 0.883

Gnomad EAS AF: 0.796

Gnomad SAS AF: 0.882

Gnomad FIN AF: 0.945

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.919

Gnomad OTH AF: 0.867

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

GnomAD4 genome AF: 0.863 AC: 131293 AN: 152168 Hom.: 57043 Cov.: 32 AF XY: 0.862 AC XY: 64156 AN XY: 74414

African (AFR) AF: 0.768 AC: 31852 AN: 41470

American (AMR) AF: 0.819 AC: 12519 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.883 AC: 3065 AN: 3472

East Asian (EAS) AF: 0.796 AC: 4108 AN: 5160

South Asian (SAS) AF: 0.881 AC: 4252 AN: 4826

European-Finnish (FIN) AF: 0.945 AC: 10039 AN: 10618

Middle Eastern (MID) AF: 0.918 AC: 270 AN: 294

European-Non Finnish (NFE) AF: 0.919 AC: 62533 AN: 68018

Other (OTH) AF: 0.869 AC: 1838 AN: 2114

Alfa AF: 0.898 Hom.: 198781

Bravo AF: 0.848

Asia WGS AF: 0.850 AC: 2956 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	1.5
DANN	Benign	0.83
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs2637496; hg19: chr5-124743267;