rs11961013

Positions:

• chr6-29504157-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.134-1164C>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 0.0363 in 152,254 control chromosomes in the GnomAD database, including 265 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 0.036 (265 hom., cov: 32)
• Consequence: LINC02829 NR_183360.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.69

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=-1.08).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02829	NR_183360.1	n.134-1164C>T		intron_variant, non_coding_transcript_variant
LINC02829	NR_183359.1	n.66-1164C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02829	ENST00000436804.2	n.66-1164C>T		intron_variant, non_coding_transcript_variant		5
LINC02829	ENST00000661850.1	n.66-1164C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0362 AC: 5514 AN: 152136 Hom.: 261 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0222

Gnomad ASJ AF: 0.0121

Gnomad EAS AF: 0.0137

Gnomad SAS AF: 0.00560

Gnomad FIN AF: 0.00217

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00869

Gnomad OTH AF: 0.0349

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

GnomAD4 genome AF: 0.0363 AC: 5528 AN: 152254 Hom.: 265 Cov.: 32 AF XY: 0.0356 AC XY: 2649 AN XY: 74450

Gnomad4 AFR AF: 0.105

Gnomad4 AMR AF: 0.0221

Gnomad4 ASJ AF: 0.0121

Gnomad4 EAS AF: 0.0137

Gnomad4 SAS AF: 0.00560

Gnomad4 FIN AF: 0.00217

Gnomad4 NFE AF: 0.00869

Gnomad4 OTH AF: 0.0346

Alfa AF: 0.0134 Hom.: 44

Bravo AF: 0.0418

Asia WGS AF: 0.0160 AC: 56 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.20
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11961013; hg19: chr6-29471934;