5-125407574-T-C

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ENSG00000248752 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.768

Gnomad4 AMR AF: 0.819

Gnomad4 ASJ AF: 0.883

Gnomad4 EAS AF: 0.796

Gnomad4 SAS AF: 0.881

Gnomad4 FIN AF: 0.945

Gnomad4 NFE AF: 0.919

Gnomad4 OTH AF: 0.869

Alfa AF: 0.904 Hom.: 82790

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2637496; hg19: chr5-124743267;