rs3130858

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_183360.1(LINC02829):​n.190+347C>A variant causes a intron, non coding transcript 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_183360.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.681

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02829	NR_183360.1	n.190+347C>A		intron_variant, non_coding_transcript_variant
LINC02829	NR_183359.1	n.122+347C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02829	ENST00000436804.2	n.122+347C>A		intron_variant, non_coding_transcript_variant		5
LINC02829	ENST00000661850.1	n.122+347C>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.919

Gnomad4 AMR AF: 0.940

Gnomad4 ASJ AF: 0.936

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.995

Gnomad4 FIN AF: 0.993

Gnomad4 NFE AF: 0.960

Gnomad4 OTH AF: 0.938

Alfa AF: 0.960 Hom.: 95833

Bravo AF: 0.944

Asia WGS AF: 0.990 AC: 3445 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3130858; hg19: chr6-29473501;