rs718979

Variant names:

• chr15-25529130-G-A
• rs718979
• ENST00000422117.1:n.168-20924C>T

Variant summary

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

The ENST00000422117.1(LINC02250):​n.168-20924C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 151,968 control chromosomes in the GnomAD database, including 12,690 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 0.40 (12690 hom., cov: 32)
• Consequence: LINC02250 ENST00000422117.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

Genes affected

LINC02250 (HGNC:53148): (long intergenic non-protein coding RNA 2250)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.531 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02250	NR_187214.1	n.183-12485C>T		intron_variant	Intron 1 of 6
LINC02250	NR_187215.1	n.183-12485C>T		intron_variant	Intron 1 of 4
LINC02250	NR_187216.1	n.183-20924C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02250	ENST00000422117.1	n.168-20924C>T		intron_variant	Intron 1 of 3	1
LINC02250	ENST00000651932.1	n.183-12485C>T		intron_variant	Intron 1 of 6
LINC02250	ENST00000655390.1	n.183-12485C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61419 AN: 151850 Hom.: 12696 Cov.: 32

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.448

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.404 AC: 61441 AN: 151968 Hom.: 12690 Cov.: 32 AF XY: 0.404 AC XY: 30034 AN XY: 74256

Gnomad4 AFR AF: 0.315

Gnomad4 AMR AF: 0.386

Gnomad4 ASJ AF: 0.410

Gnomad4 EAS AF: 0.405

Gnomad4 SAS AF: 0.548

Gnomad4 FIN AF: 0.438

Gnomad4 NFE AF: 0.448

Gnomad4 OTH AF: 0.410

Alfa AF: 0.442 Hom.: 20029

Bravo AF: 0.396

Asia WGS AF: 0.421 AC: 1467 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.7
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs718979; hg19: chr15-25774277;