rs925893

chr5-125387832-A-G

Variant summary

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

The ENST00000647105.1(LINC02240):n.384-52767A>G 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 0.509 in 151,848 control chromosomes in the GnomAD database, including 20,709 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 0.51 (20709 hom., cov: 31)
• Consequence: LINC02240 ENST00000647105.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.328

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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.663 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.384-52767A>G		intron_variant, non_coding_transcript_variant
	ENST00000655986.1	n.142+25279T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.509 AC: 77227 AN: 151730 Hom.: 20667 Cov.: 31

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.509 AC: 77325 AN: 151848 Hom.: 20709 Cov.: 31 AF XY: 0.498 AC XY: 36975 AN XY: 74176

Gnomad4 AFR AF: 0.670

Gnomad4 AMR AF: 0.429

Gnomad4 ASJ AF: 0.548

Gnomad4 EAS AF: 0.287

Gnomad4 SAS AF: 0.337

Gnomad4 FIN AF: 0.333

Gnomad4 NFE AF: 0.485

Gnomad4 OTH AF: 0.498

Alfa AF: 0.480 Hom.: 5613

Bravo AF: 0.528

Asia WGS AF: 0.370 AC: 1287 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	0.87
Dann	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs925893; hg19: chr5-124723525;