rs3131019

Positions:

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

Variant summary

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

The NR_183360.1(LINC02829):​n.134-2113C>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 0.634 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 NR_183360.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

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=-0.93).
• 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/exons	MANE	UniProt
LINC02829	NR_183360.1	n.134-2113C>A		intron_variant, non_coding_transcript_variant
LINC02829	NR_183359.1	n.66-2113C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02829	ENST00000436804.2	n.66-2113C>A		intron_variant, non_coding_transcript_variant		5
LINC02829	ENST00000661850.1	n.66-2113C>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.688

Gnomad4 AMR AF: 0.566

Gnomad4 ASJ AF: 0.511

Gnomad4 EAS AF: 0.668

Gnomad4 SAS AF: 0.784

Gnomad4 FIN AF: 0.671

Gnomad4 NFE AF: 0.606

Gnomad4 OTH AF: 0.610

Alfa AF: 0.608 Hom.: 39766

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3131019; hg19: chr6-29470985;