ENST00000486913.3:n.86-23469A>C

Variant names:

• chr5-164463200-A-C
• rs9314033
• ENST00000486913.3:n.86-23469A>C

Variant summary

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

The ENST00000486913.3(LINC03000):​n.86-23469A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.896 in 152,138 control chromosomes in the GnomAD database, including 61,261 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 0.90 (61261 hom., cov: 32)
• Consequence: LINC03000 ENST00000486913.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 4 publications found

Genes affected

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

LINC02143 (HGNC:53003): (long intergenic non-protein coding RNA 2143)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.937 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02143	NR_105064.1	n.120+1599T>G		intron_variant	Intron 2 of 3
LINC03000	XR_001742489.2	n.576+108976A>C		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03000	ENST00000486913.3	n.86-23469A>C		intron_variant	Intron 1 of 2	2
LINC03000	ENST00000517508.5	n.586-23469A>C		intron_variant	Intron 2 of 5	4
LINC03000	ENST00000519329.3	n.933-23474A>C		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.895 AC: 136126 AN: 152020 Hom.: 61205 Cov.: 32

Gnomad AFR AF: 0.945

Gnomad AMI AF: 0.927

Gnomad AMR AF: 0.916

Gnomad ASJ AF: 0.885

Gnomad EAS AF: 0.659

Gnomad SAS AF: 0.872

Gnomad FIN AF: 0.855

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.886

Gnomad OTH AF: 0.901

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

GnomAD4 genome AF: 0.896 AC: 136240 AN: 152138 Hom.: 61261 Cov.: 32 AF XY: 0.894 AC XY: 66503 AN XY: 74364

African (AFR) AF: 0.945 AC: 39270 AN: 41544

American (AMR) AF: 0.917 AC: 13994 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.885 AC: 3070 AN: 3470

East Asian (EAS) AF: 0.659 AC: 3394 AN: 5154

South Asian (SAS) AF: 0.872 AC: 4201 AN: 4820

European-Finnish (FIN) AF: 0.855 AC: 9053 AN: 10590

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.886 AC: 60248 AN: 67970

Other (OTH) AF: 0.898 AC: 1901 AN: 2116

Alfa AF: 0.894 Hom.: 4752

Bravo AF: 0.899

Asia WGS AF: 0.788 AC: 2743 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.69
DANN	Benign	0.53
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs9314033; hg19: chr5-163890206;