rs3131019

Variant names:

• chr6-29503208-C-A
• rs3131019
• ENST00000436804.3:n.68-2113C>A

Your query was ambiguous. Multiple possible variants found:

• chr6-29503208-C-A
• chr6-29503208-C-G

Variant summary

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

The ENST00000436804.3(LINC02829):​n.68-2113C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.634 in 152,166 control chromosomes in the GnomAD database, including 30,851 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 0.63 (30851 hom., cov: 33)
• Consequence: LINC02829 ENST00000436804.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 16 publications found

Genes affected

LINC02829 (HGNC:54362): (long intergenic non-protein coding RNA 2829)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02829	NR_183359.1	n.66-2113C>A		intron_variant	Intron 1 of 3
LINC02829	NR_183360.1	n.134-2113C>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02829	ENST00000436804.3	n.68-2113C>A		intron_variant	Intron 1 of 3	5
LINC02829	ENST00000661850.2	n.197-2113C>A		intron_variant	Intron 1 of 2
LINC02829	ENST00000824900.1	n.136-2113C>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.634 AC: 96347 AN: 152048 Hom.: 30808 Cov.: 33

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.668

Gnomad SAS AF: 0.786

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.634 AC: 96447 AN: 152166 Hom.: 30851 Cov.: 33 AF XY: 0.637 AC XY: 47380 AN XY: 74372

African (AFR) AF: 0.688 AC: 28566 AN: 41534

American (AMR) AF: 0.566 AC: 8653 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.511 AC: 1773 AN: 3472

East Asian (EAS) AF: 0.668 AC: 3452 AN: 5170

South Asian (SAS) AF: 0.784 AC: 3778 AN: 4820

European-Finnish (FIN) AF: 0.671 AC: 7099 AN: 10584

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.606 AC: 41167 AN: 67980

Other (OTH) AF: 0.610 AC: 1288 AN: 2110

Alfa AF: 0.617 Hom.: 75506

Bravo AF: 0.627

Asia WGS AF: 0.762 AC: 2651 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.6
DANN	Benign	0.65
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs3131019; hg19: chr6-29470985;