5-164552322-C-A

Variant names:

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

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000486913.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03000	ENST00000486913.3	TSL:2	n.159-48653C>A		intron	N/A
	LINC03000	ENST00000517508.5	TSL:4	n.716+28318C>A		intron	N/A
	LINC03000	ENST00000519570.5	TSL:3	n.304-170443C>A		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs726336;

hg19: chr5-163979328;