rs3130858

Variant names:

• chr6-29505724-C-A
• rs3130858
• ENST00000436804.3:n.124+347C>A

Your query was ambiguous. Multiple possible variants found:

• chr6-29505724-C-A
• chr6-29505724-C-G
• chr6-29505724-C-T

Variant summary

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

The NR_183359.1(LINC02829):​n.122+347C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.951 in 152,212 control chromosomes in the GnomAD database, including 68,851 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 0.95 (68851 hom., cov: 31)
• Consequence: LINC02829 NR_183359.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.681
• Publications: 10 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_183359.1. 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
	LINC02829	NR_183359.1		n.122+347C>A		intron	N/A
	LINC02829	NR_183360.1		n.190+347C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02829	ENST00000436804.3	TSL:5	n.124+347C>A		intron	N/A
	LINC02829	ENST00000661850.2		n.253+347C>A		intron	N/A
	LINC02829	ENST00000824900.1		n.192+347C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.951 AC: 144597 AN: 152094 Hom.: 68791 Cov.: 31

Gnomad AFR AF: 0.918

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.940

Gnomad ASJ AF: 0.936

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.995

Gnomad FIN AF: 0.993

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.960

Gnomad OTH AF: 0.937

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

GnomAD4 genome AF: 0.951 AC: 144716 AN: 152212 Hom.: 68851 Cov.: 31 AF XY: 0.953 AC XY: 70937 AN XY: 74404

African (AFR) AF: 0.919 AC: 38107 AN: 41488

American (AMR) AF: 0.940 AC: 14374 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.936 AC: 3249 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5174 AN: 5176

South Asian (SAS) AF: 0.995 AC: 4795 AN: 4818

European-Finnish (FIN) AF: 0.993 AC: 10551 AN: 10624

Middle Eastern (MID) AF: 0.949 AC: 279 AN: 294

European-Non Finnish (NFE) AF: 0.960 AC: 65291 AN: 68014

Other (OTH) AF: 0.938 AC: 1985 AN: 2116

Alfa AF: 0.957 Hom.: 176989

Bravo AF: 0.944

Asia WGS AF: 0.990 AC: 3445 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.81
DANN	Benign	0.55
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs3130858; hg19: chr6-29473501;