5-165119891-A-G

Variant names:

• chr5-165119891-A-G
• rs10515889
• ENST00000519267.1:n.118-9923A>G

Variant summary

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

The ENST00000519267.1(LINC03000):​n.118-9923A>G variant causes a intron 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 ENST00000519267.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.255
• Publications: 6 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000519267.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03000	ENST00000519267.1	TSL:3	n.118-9923A>G		intron	N/A
	LINC03000	ENST00000519570.5	TSL:3	n.452-51487A>G		intron	N/A
	LINC03000	ENST00000522303.5	TSL:5	n.291-51487A>G		intron	N/A

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

African (AFR) AF: 0.109 AC: 4549 AN: 41544

American (AMR) AF: 0.0991 AC: 1512 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 411 AN: 3466

East Asian (EAS) AF: 0.209 AC: 1075 AN: 5150

South Asian (SAS) AF: 0.0638 AC: 308 AN: 4830

European-Finnish (FIN) AF: 0.127 AC: 1346 AN: 10596

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.143 AC: 9697 AN: 67998

Other (OTH) AF: 0.113 AC: 239 AN: 2112

Alfa AF: 0.134 Hom.: 759

Bravo AF: 0.127

Asia WGS AF: 0.125 AC: 433 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.47
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs10515889; hg19: chr5-164546897;