rs726336

chr5-164552322-C-Achr5-164552322-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000519570.5(LINC03000):n.304-170443C>A variant causes a intron, non coding transcript 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 ENST00000519570.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.57

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC03000	XR_001742489.2	n.577-170443C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC03000	ENST00000519570.5	n.304-170443C>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.690

Gnomad4 AMR AF: 0.583

Gnomad4 ASJ AF: 0.609

Gnomad4 EAS AF: 0.463

Gnomad4 SAS AF: 0.472

Gnomad4 FIN AF: 0.624

Gnomad4 NFE AF: 0.568

Gnomad4 OTH AF: 0.592

Alfa AF: 0.602 Hom.: 3990

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs726336; hg19: chr5-163979328;