rs4325129

Variant names:

• chr1-159492591-A-G
• rs4325129
• ENST00000732995.1:n.392+9607A>G

Variant summary

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

The ENST00000732995.1(LINC02819):​n.392+9607A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 152,218 control chromosomes in the GnomAD database, including 2,469 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 (2469 hom., cov: 32)
• Consequence: LINC02819 ENST00000732995.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 9 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=-0.89).
• 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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02819	ENST00000732995.1	n.392+9607A>G		intron_variant	Intron 2 of 3
LINC02819	ENST00000733001.1	n.217+9607A>G		intron_variant	Intron 2 of 3
LINC02819	ENST00000733002.1	n.81+9607A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24241 AN: 152100 Hom.: 2468 Cov.: 32

Gnomad AFR AF: 0.0512

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.0781

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.159 AC: 24249 AN: 152218 Hom.: 2469 Cov.: 32 AF XY: 0.162 AC XY: 12059 AN XY: 74406

African (AFR) AF: 0.0511 AC: 2124 AN: 41564

American (AMR) AF: 0.180 AC: 2752 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 386 AN: 3470

East Asian (EAS) AF: 0.0779 AC: 404 AN: 5188

South Asian (SAS) AF: 0.136 AC: 659 AN: 4830

European-Finnish (FIN) AF: 0.280 AC: 2963 AN: 10576

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

European-Non Finnish (NFE) AF: 0.214 AC: 14524 AN: 67988

Other (OTH) AF: 0.145 AC: 305 AN: 2108

Alfa AF: 0.186 Hom.: 8329

Bravo AF: 0.146

Asia WGS AF: 0.104 AC: 364 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.27
DANN	Benign	0.69
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4325129; hg19: chr1-159462381;