1-159484147-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02819	XR_922189.4	n.687+1163C>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02819	ENST00000732995.1	n.392+1163C>T		intron_variant	Intron 2 of 3
LINC02819	ENST00000733001.1	n.217+1163C>T		intron_variant	Intron 2 of 3
LINC02819	ENST00000733002.1	n.81+1163C>T		intron_variant	Intron 1 of 3

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 v4.3

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;