rs1233482

Positions:

• chr6-29507905-C-A

Variant summary

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

The ENST00000661850.1(LINC02829):​n.859C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 152,116 control chromosomes in the GnomAD database, including 4,155 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 0.21 (4155 hom., cov: 33)
• Consequence: LINC02829 ENST00000661850.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.430

Genes affected

LINC02829 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02829	NR_183359.1	n.622+237C>A		intron_variant
LINC02829	NR_183360.1	n.690+237C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02829	ENST00000661850.1	n.859C>A		non_coding_transcript_exon_variant	3/3
LINC02829	ENST00000436804.2	n.622+237C>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32246 AN: 151996 Hom.: 4142 Cov.: 33

Gnomad AFR AF: 0.0808

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.212 AC: 32263 AN: 152116 Hom.: 4155 Cov.: 33 AF XY: 0.219 AC XY: 16249 AN XY: 74328

Gnomad4 AFR AF: 0.0808

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.159

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.324

Gnomad4 FIN AF: 0.410

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.209

Alfa AF: 0.252 Hom.: 6616

Bravo AF: 0.184

Asia WGS AF: 0.308 AC: 1070 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.73
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1233482; hg19: chr6-29475682;