rs3131020

Positions:

• chr6-29508125-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.690+457C>T 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 0.473 in 151,962 control chromosomes in the GnomAD database, including 17,476 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 0.47 (17476 hom., cov: 32)
• Consequence: LINC02829 NR_183360.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.432

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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.583 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02829	NR_183360.1	n.690+457C>T		intron_variant, non_coding_transcript_variant
LINC02829	NR_183359.1	n.622+457C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02829	ENST00000436804.2	n.622+457C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71743 AN: 151844 Hom.: 17444 Cov.: 32

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.473 AC: 71820 AN: 151962 Hom.: 17476 Cov.: 32 AF XY: 0.473 AC XY: 35164 AN XY: 74276

Gnomad4 AFR AF: 0.562

Gnomad4 AMR AF: 0.360

Gnomad4 ASJ AF: 0.313

Gnomad4 EAS AF: 0.382

Gnomad4 SAS AF: 0.601

Gnomad4 FIN AF: 0.521

Gnomad4 NFE AF: 0.444

Gnomad4 OTH AF: 0.434

Alfa AF: 0.443 Hom.: 25571

Bravo AF: 0.460

Asia WGS AF: 0.584 AC: 2028 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	4.7
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3131020; hg19: chr6-29475902;