chr1-159484147-C-T

Variant names:

• chr1-159484147-C-T
• rs4133289
• ENST00000732995.1:n.392+1163C>T

Variant summary

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

The ENST00000732995.1(LINC02819):​n.392+1163C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 152,174 control chromosomes in the GnomAD database, including 2,428 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 0.16 (2428 hom., cov: 32)
• Consequence: LINC02819 ENST00000732995.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.470
• Publications: 12 publications found

Genes affected

LINC02819 (HGNC:54350): (long intergenic non-protein coding RNA 2819)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000732995.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02819	ENST00000732995.1		n.392+1163C>T		intron	N/A
	LINC02819	ENST00000733001.1		n.217+1163C>T		intron	N/A
	LINC02819	ENST00000733002.1		n.81+1163C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23767 AN: 152056 Hom.: 2427 Cov.: 32

Gnomad AFR AF: 0.0490

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.0192

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.156 AC: 23776 AN: 152174 Hom.: 2428 Cov.: 32 AF XY: 0.159 AC XY: 11804 AN XY: 74400

African (AFR) AF: 0.0490 AC: 2035 AN: 41542

American (AMR) AF: 0.179 AC: 2740 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 390 AN: 3468

East Asian (EAS) AF: 0.0193 AC: 100 AN: 5184

South Asian (SAS) AF: 0.130 AC: 624 AN: 4818

European-Finnish (FIN) AF: 0.278 AC: 2940 AN: 10570

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.214 AC: 14524 AN: 67992

Other (OTH) AF: 0.138 AC: 291 AN: 2112

Alfa AF: 0.187 Hom.: 9984

Bravo AF: 0.143

Asia WGS AF: 0.0830 AC: 293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.7
DANN	Benign	0.70
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs4133289; hg19: chr1-159453937;