chr8-11234743-G-C

Position:

• chr8-11234743-G-C

Variant summary

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

The ENST00000711291.1(LINC00529):​n.378+12883C>G variant causes a intron, non coding transcript 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 ENST00000711291.1 intron, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00529	ENST00000711291.1	n.378+12883C>G		intron_variant, non_coding_transcript_variant
LINC00529	ENST00000443854.2	n.300+12883C>G		intron_variant, non_coding_transcript_variant		2

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;