rs1529079

Variant names:

• chr3-34502768-G-A
• rs1529079
• ENST00000424786.5:n.571-53820G>A

Variant summary

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

The ENST00000424786.5(LINC01811):​n.571-53820G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 152,062 control chromosomes in the GnomAD database, including 2,732 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 0.18 (2732 hom., cov: 32)
• Consequence: LINC01811 ENST00000424786.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96
• Publications: 0 publications found

Genes affected

LINC01811 (HGNC:52615): (long intergenic non-protein coding RNA 1811)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.23 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
LINC01811	ENST00000424786.5	n.571-53820G>A		intron_variant	Intron 6 of 7	5
LINC01811	ENST00000655650.1	n.310-48639G>A		intron_variant	Intron 3 of 6
LINC01811	ENST00000656055.1	n.542-48634G>A		intron_variant	Intron 5 of 9

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27623 AN: 151944 Hom.: 2726 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.0559

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.182 AC: 27658 AN: 152062 Hom.: 2732 Cov.: 32 AF XY: 0.186 AC XY: 13796 AN XY: 74330

African (AFR) AF: 0.234 AC: 9693 AN: 41448

American (AMR) AF: 0.222 AC: 3383 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0559 AC: 194 AN: 3472

East Asian (EAS) AF: 0.177 AC: 915 AN: 5176

South Asian (SAS) AF: 0.200 AC: 962 AN: 4822

European-Finnish (FIN) AF: 0.248 AC: 2622 AN: 10576

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.138 AC: 9390 AN: 67984

Other (OTH) AF: 0.169 AC: 357 AN: 2112

Alfa AF: 0.157 Hom.: 2999

Bravo AF: 0.187

Asia WGS AF: 0.183 AC: 636 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.14
DANN	Benign	0.54
PhyloP100		-2.0
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs1529079; hg19: chr3-34544260;