8-11260256-G-C

Variant names:

• chr8-11260256-G-C
• rs2736376
• ENST00000443854.2:n.136+7533C>G

Variant summary

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

The ENST00000443854.2(LINC00529):​n.136+7533C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 151,880 control chromosomes in the GnomAD database, including 3,951 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 (3951 hom., cov: 32)
• Consequence: LINC00529 ENST00000443854.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.274
• Publications: 4 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00529	NR_170283.1	n.558+7533C>G		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00529	ENST00000443854.2	n.136+7533C>G		intron_variant	Intron 2 of 5	2
LINC00529	ENST00000711291.1	n.214+7021C>G		intron_variant	Intron 3 of 7

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31137 AN: 151762 Hom.: 3930 Cov.: 32

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.205 AC: 31197 AN: 151880 Hom.: 3951 Cov.: 32 AF XY: 0.205 AC XY: 15228 AN XY: 74228

African (AFR) AF: 0.341 AC: 14126 AN: 41424

American (AMR) AF: 0.294 AC: 4492 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 731 AN: 3472

East Asian (EAS) AF: 0.141 AC: 729 AN: 5176

South Asian (SAS) AF: 0.154 AC: 738 AN: 4804

European-Finnish (FIN) AF: 0.130 AC: 1368 AN: 10518

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8397 AN: 67908

Other (OTH) AF: 0.230 AC: 485 AN: 2110

Alfa AF: 0.0684 Hom.: 77

Bravo AF: 0.228

Asia WGS AF: 0.180 AC: 621 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.5
DANN	Benign	0.55
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs2736376; hg19: chr8-11117765;