5-125428454-G-A

Variant names:

• chr5-125428454-G-A
• rs2637502
• ENST00000647105.1:n.384-12145G>A

Variant summary

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

The ENST00000647105.1(LINC02240):​n.384-12145G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.376 in 151,918 control chromosomes in the GnomAD database, including 12,203 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 0.38 (12203 hom., cov: 32)
• Consequence: LINC02240 ENST00000647105.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 0 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 (AMR) allele frequency at 95% confidence interval = 0.473 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.384-12145G>A		intron_variant	Intron 3 of 6
ENSG00000248752	ENST00000651847.1	n.1077-1694C>T		intron_variant	Intron 12 of 15
ENSG00000248752	ENST00000825443.1	n.553-1694C>T		intron_variant	Intron 6 of 7

Frequencies

GnomAD3 genomes AF: 0.376 AC: 57049 AN: 151800 Hom.: 12196 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.376 AC: 57070 AN: 151918 Hom.: 12203 Cov.: 32 AF XY: 0.376 AC XY: 27887 AN XY: 74260

African (AFR) AF: 0.172 AC: 7130 AN: 41468

American (AMR) AF: 0.482 AC: 7351 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.539 AC: 1869 AN: 3466

East Asian (EAS) AF: 0.164 AC: 850 AN: 5168

South Asian (SAS) AF: 0.332 AC: 1600 AN: 4822

European-Finnish (FIN) AF: 0.455 AC: 4789 AN: 10524

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.473 AC: 32109 AN: 67918

Other (OTH) AF: 0.396 AC: 830 AN: 2098

Alfa AF: 0.424 Hom.: 4118

Bravo AF: 0.371

Asia WGS AF: 0.275 AC: 955 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.9
DANN	Benign	0.63
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs2637502; hg19: chr5-124764147;