rs2251301

Positions:

• chr8-11261528-C-T

Variant summary

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

The NR_170283.1(LINC00529):​n.558+6261G>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 0.117 in 152,236 control chromosomes in the GnomAD database, including 1,270 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 0.12 (1270 hom., cov: 33)
• Consequence: LINC00529 NR_170283.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.470

Genes affected

LINC00529 (HGNC:15544): (long intergenic non-protein coding RNA 529)

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 (NFE) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00529	NR_170283.1	n.558+6261G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00529	ENST00000711291.1	n.214+5749G>A		intron_variant, non_coding_transcript_variant
LINC00529	ENST00000443854.2	n.136+6261G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17797 AN: 152118 Hom.: 1269 Cov.: 33

Gnomad AFR AF: 0.0470

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.0826

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.117 AC: 17800 AN: 152236 Hom.: 1270 Cov.: 33 AF XY: 0.116 AC XY: 8604 AN XY: 74448

Gnomad4 AFR AF: 0.0469

Gnomad4 AMR AF: 0.0825

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.00251

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.104

Alfa AF: 0.149 Hom.: 4046

Bravo AF: 0.104

Asia WGS AF: 0.0680 AC: 241 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2251301; hg19: chr8-11119037;