rs10502449

Variant names:

• chr18-24589283-G-A
• rs10502449
• ENST00000664008.1:n.511+54222G>A

Variant summary

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

The ENST00000664008.1(LINC01915):​n.511+54222G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0342 in 152,214 control chromosomes in the GnomAD database, including 225 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 0.034 (225 hom., cov: 32)
• Consequence: LINC01915 ENST00000664008.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.632

Genes affected

LINC01915 (HGNC:52734): (long intergenic non-protein coding RNA 1915)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0763 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
LINC01915	ENST00000664008.1	n.511+54222G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0342 AC: 5199 AN: 152096 Hom.: 224 Cov.: 32

Gnomad AFR AF: 0.0741

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0802

Gnomad ASJ AF: 0.00490

Gnomad EAS AF: 0.0731

Gnomad SAS AF: 0.0568

Gnomad FIN AF: 0.00160

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00237

Gnomad OTH AF: 0.0277

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

GnomAD4 genome AF: 0.0342 AC: 5207 AN: 152214 Hom.: 225 Cov.: 32 AF XY: 0.0361 AC XY: 2685 AN XY: 74420

Gnomad4 AFR AF: 0.0741

Gnomad4 AMR AF: 0.0800

Gnomad4 ASJ AF: 0.00490

Gnomad4 EAS AF: 0.0733

Gnomad4 SAS AF: 0.0565

Gnomad4 FIN AF: 0.00160

Gnomad4 NFE AF: 0.00237

Gnomad4 OTH AF: 0.0284

Alfa AF: 0.0180 Hom.: 13

Bravo AF: 0.0412

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.58
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10502449; hg19: chr18-22169247;