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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000443854.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00529	ENST00000443854.2	TSL:2	n.300+12883C>T		intron	N/A
	LINC00529	ENST00000711291.1		n.378+12883C>T		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2572406;

hg19: chr8-11092252;