rs2572406

Variant names:

• chr8-11234743-G-A
• rs2572406
• ENST00000443854.2:n.300+12883C>T

Your query was ambiguous. Multiple possible variants found:

• chr8-11234743-G-A
• chr8-11234743-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000443854.2(LINC00529):​n.300+12883C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00682 in 152,104 control chromosomes in the GnomAD database, including 9 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 0.0068 (9 hom., cov: 32)
• Consequence: LINC00529 ENST00000443854.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.243
• Publications: 8 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).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00682 (1038/152104) while in subpopulation AFR AF = 0.0188 (781/41496). AF 95% confidence interval is 0.0177. There are 9 homozygotes in GnomAd4. There are 514 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 9 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00529	ENST00000443854.2	n.300+12883C>T		intron_variant	Intron 3 of 5	2
LINC00529	ENST00000711291.1	n.378+12883C>T		intron_variant	Intron 4 of 7

Frequencies

GnomAD3 genomes AF: 0.00680 AC: 1033 AN: 151986 Hom.: 8 Cov.: 32

Gnomad AFR AF: 0.0188

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0113

Gnomad ASJ AF: 0.00288

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000809

Gnomad OTH AF: 0.00813

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

GnomAD4 genome AF: 0.00682 AC: 1038 AN: 152104 Hom.: 9 Cov.: 32 AF XY: 0.00691 AC XY: 514 AN XY: 74336

African (AFR) AF: 0.0188 AC: 781 AN: 41496

American (AMR) AF: 0.0114 AC: 174 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.00288 AC: 10 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5172

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4822

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10548

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 292

European-Non Finnish (NFE) AF: 0.000809 AC: 55 AN: 67994

Other (OTH) AF: 0.00805 AC: 17 AN: 2112

Alfa AF: 0.00 Hom.: 1067

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.92
DANN	Benign	0.54
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs2572406; hg19: chr8-11092252;