6-29501032-A-G

Position:

• chr6-29501032-A-G

Variant summary

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

The NR_183360.1(LINC02829):​n.133+2816A>G 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 0.239 in 152,164 control chromosomes in the GnomAD database, including 4,396 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 0.24 (4396 hom., cov: 33)
• Consequence: LINC02829 NR_183360.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.215

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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02829	NR_183360.1	n.133+2816A>G		intron_variant, non_coding_transcript_variant
LINC02829	NR_183359.1	n.65+3493A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02829	ENST00000436804.2	n.65+3493A>G		intron_variant, non_coding_transcript_variant		5
LINC02829	ENST00000661850.1	n.65+3493A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36300 AN: 152046 Hom.: 4390 Cov.: 33

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.175

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.239 AC: 36328 AN: 152164 Hom.: 4396 Cov.: 33 AF XY: 0.234 AC XY: 17390 AN XY: 74414

Gnomad4 AFR AF: 0.237

Gnomad4 AMR AF: 0.238

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.235

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.188

Gnomad4 NFE AF: 0.257

Gnomad4 OTH AF: 0.219

Alfa AF: 0.253 Hom.: 9381

Bravo AF: 0.249

Asia WGS AF: 0.161 AC: 561 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	7.7
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: rs1233487; hg19: chr6-29468809;