rs925893

Variant names:

• chr5-125387832-A-G
• rs925893
• ENST00000647105.1:n.384-52767A>G

Variant summary

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

The ENST00000647105.1(LINC02240):​n.384-52767A>G variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.328
• Publications: 4 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=-0.81).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02240	ENST00000647105.1	n.384-52767A>G		intron_variant	Intron 3 of 6
ENSG00000248752	ENST00000655986.1	n.142+25279T>C		intron_variant	Intron 1 of 1
LINC02240	ENST00000825647.1	n.112+29626A>G		intron_variant	Intron 1 of 3

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

African (AFR) AF: 0.670 AC: 27747 AN: 41430

American (AMR) AF: 0.429 AC: 6542 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.548 AC: 1896 AN: 3460

East Asian (EAS) AF: 0.287 AC: 1482 AN: 5158

South Asian (SAS) AF: 0.337 AC: 1624 AN: 4814

European-Finnish (FIN) AF: 0.333 AC: 3512 AN: 10536

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.485 AC: 32911 AN: 67886

Other (OTH) AF: 0.498 AC: 1048 AN: 2106

Alfa AF: 0.491 Hom.: 7438

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
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs925893; hg19: chr5-124723525;