8-11234743-G-C

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000443854.2(LINC00529):​n.300+12883C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.488 in 152,036 control chromosomes in the GnomAD database, including 18,322 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 0.49 (18322 hom., cov: 32)
• Consequence: LINC00529 ENST00000443854.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.243

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.522 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+12883C>G		intron_variant	Intron 3 of 5	2
LINC00529	ENST00000711291.1	n.378+12883C>G		intron_variant	Intron 4 of 7

Frequencies

GnomAD3 genomes AF: 0.488 AC: 74082 AN: 151918 Hom.: 18299 Cov.: 32

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.361

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.485

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

GnomAD4 genome AF: 0.488 AC: 74161 AN: 152036 Hom.: 18322 Cov.: 32 AF XY: 0.487 AC XY: 36174 AN XY: 74290

Gnomad4 AFR AF: 0.442

Gnomad4 AMR AF: 0.531

Gnomad4 ASJ AF: 0.584

Gnomad4 EAS AF: 0.454

Gnomad4 SAS AF: 0.358

Gnomad4 FIN AF: 0.485

Gnomad4 NFE AF: 0.515

Gnomad4 OTH AF: 0.488

Alfa AF: 0.384 Hom.: 1067

Bravo AF: 0.493

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.77
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2572406; hg19: chr8-11092252;