chr8-11246602-G-A

Variant names:

• chr8-11246602-G-A
• rs7824557
• ENST00000443854.2:n.300+1024C>T

Variant summary

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

The ENST00000443854.2(LINC00529):​n.300+1024C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.675 in 152,004 control chromosomes in the GnomAD database, including 35,451 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 0.67 (35451 hom., cov: 31)
• Consequence: LINC00529 ENST00000443854.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.517

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 (AFR) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

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+1024C>T		intron_variant	Intron 3 of 5	2
LINC00529	ENST00000711291.1	n.378+1024C>T		intron_variant	Intron 4 of 7

Frequencies

GnomAD3 genomes AF: 0.674 AC: 102414 AN: 151886 Hom.: 35395 Cov.: 31

Gnomad AFR AF: 0.829

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.599

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.635

Gnomad NFE AF: 0.612

Gnomad OTH AF: 0.662

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

GnomAD4 genome AF: 0.675 AC: 102533 AN: 152004 Hom.: 35451 Cov.: 31 AF XY: 0.671 AC XY: 49878 AN XY: 74286

African (AFR) AF: 0.829 AC: 34371 AN: 41480

American (AMR) AF: 0.707 AC: 10810 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.688 AC: 2386 AN: 3470

East Asian (EAS) AF: 0.600 AC: 3102 AN: 5166

South Asian (SAS) AF: 0.533 AC: 2566 AN: 4816

European-Finnish (FIN) AF: 0.540 AC: 5680 AN: 10518

Middle Eastern (MID) AF: 0.634 AC: 184 AN: 290

European-Non Finnish (NFE) AF: 0.612 AC: 41608 AN: 67952

Other (OTH) AF: 0.662 AC: 1395 AN: 2106

Alfa AF: 0.636 Hom.: 105310

Bravo AF: 0.691

Asia WGS AF: 0.592 AC: 2059 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.1
DANN	Benign	0.52
PhyloP100		0.52

Splicing

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

Publications

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Other links and lift over

dbSNP: rs7824557; hg19: chr8-11104111;