rs726336

Variant names:

• chr5-164552322-C-A
• rs726336
• ENST00000486913.3:n.159-48653C>A

Your query was ambiguous. Multiple possible variants found:

• chr5-164552322-C-A
• chr5-164552322-C-T

Variant summary

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

The ENST00000486913.3(LINC03000):​n.159-48653C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.601 in 151,978 control chromosomes in the GnomAD database, including 27,778 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 0.60 (27778 hom., cov: 32)
• Consequence: LINC03000 ENST00000486913.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.57
• Publications: 3 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=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC03000	XR_001742489.2	n.577-170443C>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03000	ENST00000486913.3	n.159-48653C>A		intron_variant	Intron 2 of 2	2
LINC03000	ENST00000517508.5	n.716+28318C>A		intron_variant	Intron 4 of 5	4
LINC03000	ENST00000519570.5	n.304-170443C>A		intron_variant	Intron 2 of 5	3

Frequencies

GnomAD3 genomes AF: 0.601 AC: 91283 AN: 151858 Hom.: 27743 Cov.: 32

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.593

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

GnomAD4 genome AF: 0.601 AC: 91379 AN: 151978 Hom.: 27778 Cov.: 32 AF XY: 0.600 AC XY: 44579 AN XY: 74272

African (AFR) AF: 0.690 AC: 28608 AN: 41444

American (AMR) AF: 0.583 AC: 8899 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.609 AC: 2108 AN: 3464

East Asian (EAS) AF: 0.463 AC: 2395 AN: 5172

South Asian (SAS) AF: 0.472 AC: 2277 AN: 4820

European-Finnish (FIN) AF: 0.624 AC: 6596 AN: 10564

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.568 AC: 38555 AN: 67936

Other (OTH) AF: 0.592 AC: 1247 AN: 2106

Alfa AF: 0.604 Hom.: 4168

Bravo AF: 0.607

Asia WGS AF: 0.507 AC: 1763 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.058
DANN	Benign	0.19
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs726336; hg19: chr5-163979328;