rs2913719

Variant names:

• chr5-164588189-T-C
• rs2913719
• ENST00000486913.3:n.159-12786T>C

Variant summary

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

The ENST00000486913.3(LINC03000):​n.159-12786T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,080 control chromosomes in the GnomAD database, including 2,517 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 0.10 (2517 hom., cov: 32)
• Consequence: LINC03000 ENST00000486913.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.265
• Publications: 4 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC03000	XR_001742489.2	n.577-134576T>C		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03000	ENST00000486913.3	n.159-12786T>C		intron_variant	Intron 2 of 2	2
LINC03000	ENST00000517508.5	n.716+64185T>C		intron_variant	Intron 4 of 5	4
LINC03000	ENST00000519570.5	n.304-134576T>C		intron_variant	Intron 2 of 5	3

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15330 AN: 151960 Hom.: 2512 Cov.: 32

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0369

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0291

Gnomad SAS AF: 0.00517

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0170

Gnomad NFE AF: 0.00172

Gnomad OTH AF: 0.0750

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

GnomAD4 genome AF: 0.101 AC: 15370 AN: 152080 Hom.: 2517 Cov.: 32 AF XY: 0.0979 AC XY: 7278 AN XY: 74356

African (AFR) AF: 0.346 AC: 14352 AN: 41454

American (AMR) AF: 0.0369 AC: 564 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3468

East Asian (EAS) AF: 0.0292 AC: 151 AN: 5176

South Asian (SAS) AF: 0.00497 AC: 24 AN: 4826

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10614

Middle Eastern (MID) AF: 0.0181 AC: 5 AN: 276

European-Non Finnish (NFE) AF: 0.00172 AC: 117 AN: 67948

Other (OTH) AF: 0.0742 AC: 157 AN: 2116

Alfa AF: 0.0923 Hom.: 271

Bravo AF: 0.115

Asia WGS AF: 0.0380 AC: 130 AN: 3434

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.0
DANN	Benign	0.43
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs2913719; hg19: chr5-164015195;