rs2913719

Positions:

• chr5-164588189-T-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LINC03000 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC03000	XR_001742489.2	n.577-134576T>C		intron_variant

Ensembl

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

Gnomad4 AFR AF: 0.346

Gnomad4 AMR AF: 0.0369

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.0292

Gnomad4 SAS AF: 0.00497

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00172

Gnomad4 OTH AF: 0.0742

Alfa AF: 0.0834 Hom.: 238

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2913719; hg19: chr5-164015195;