chr5-125428454-G-A

Position:

• chr5-125428454-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000647105.1(LINC02240):​n.384-12145G>A variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02240	ENST00000647105.1	n.384-12145G>A		intron_variant, non_coding_transcript_variant
	ENST00000651847.1	n.1077-1694C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.482

Gnomad4 ASJ AF: 0.539

Gnomad4 EAS AF: 0.164

Gnomad4 SAS AF: 0.332

Gnomad4 FIN AF: 0.455

Gnomad4 NFE AF: 0.473

Gnomad4 OTH AF: 0.396

Alfa AF: 0.422 Hom.: 3316

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2637502; hg19: chr5-124764147;