rs2251301

Variant names:

• chr8-11261528-C-T
• rs2251301
• ENST00000443854.2:n.136+6261G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000443854.2(LINC00529):​n.136+6261G>A variant causes a intron 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 ENST00000443854.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.470
• Publications: 18 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC00529	NR_170283.1	n.558+6261G>A		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00529	ENST00000443854.2	n.136+6261G>A		intron_variant	Intron 2 of 5	2
LINC00529	ENST00000711291.1	n.214+5749G>A		intron_variant	Intron 3 of 7

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

African (AFR) AF: 0.0469 AC: 1950 AN: 41560

American (AMR) AF: 0.0825 AC: 1262 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 718 AN: 3470

East Asian (EAS) AF: 0.00251 AC: 13 AN: 5186

South Asian (SAS) AF: 0.152 AC: 734 AN: 4814

European-Finnish (FIN) AF: 0.136 AC: 1446 AN: 10602

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.167 AC: 11332 AN: 67984

Other (OTH) AF: 0.104 AC: 220 AN: 2114

Alfa AF: 0.142 Hom.: 5267

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
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs2251301; hg19: chr8-11119037;