rs10502449

chr18-24589283-G-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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01915	ENST00000664008.1	n.511+54222G>A		intron_variant, non_coding_transcript_variant

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;