rs10515889

chr5-165119891-A-Gchr5-165119891-A-T

Variant summary

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

The ENST00000519570.5(LINC03000):n.452-51487A>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 0.127 in 152,166 control chromosomes in the GnomAD database, including 1,259 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 0.13 (1259 hom., cov: 32)
• Consequence: LINC03000 ENST00000519570.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.255

Genes affected

LINC03000 (HGNC:56116): (long intergenic non-protein coding RNA 3000)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.198 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
LINC03000	ENST00000519570.5	n.452-51487A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19241 AN: 152048 Hom.: 1256 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.0993

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.0631

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.127 AC: 19253 AN: 152166 Hom.: 1259 Cov.: 32 AF XY: 0.125 AC XY: 9295 AN XY: 74400

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.0991

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.209

Gnomad4 SAS AF: 0.0638

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.143

Gnomad4 OTH AF: 0.113

Alfa AF: 0.134 Hom.: 684

Bravo AF: 0.127

Asia WGS AF: 0.125 AC: 433 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.2
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10515889; hg19: chr5-164546897;