11-104517986-T-G

Variant names:

• chr11-104517986-T-G
• rs1487683
• ENST00000536529.5:n.423-5753A>C

Variant summary

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

The ENST00000536529.5(LINC02552):​n.423-5753A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.829 in 151,816 control chromosomes in the GnomAD database, including 52,493 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 0.83 (52493 hom., cov: 29)
• Consequence: LINC02552 ENST00000536529.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980

Genes affected

LINC02552 (HGNC:53587): (long intergenic non-protein coding RNA 2552)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.889 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
LINC02552	ENST00000536529.5	n.423-5753A>C		intron_variant	Intron 3 of 4	3

Frequencies

GnomAD3 genomes AF: 0.829 AC: 125828 AN: 151698 Hom.: 52465 Cov.: 29

Gnomad AFR AF: 0.749

Gnomad AMI AF: 0.859

Gnomad AMR AF: 0.902

Gnomad ASJ AF: 0.820

Gnomad EAS AF: 0.838

Gnomad SAS AF: 0.817

Gnomad FIN AF: 0.819

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.863

Gnomad OTH AF: 0.850

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

GnomAD4 genome AF: 0.829 AC: 125907 AN: 151816 Hom.: 52493 Cov.: 29 AF XY: 0.831 AC XY: 61599 AN XY: 74150

Gnomad4 AFR AF: 0.749

Gnomad4 AMR AF: 0.902

Gnomad4 ASJ AF: 0.820

Gnomad4 EAS AF: 0.837

Gnomad4 SAS AF: 0.817

Gnomad4 FIN AF: 0.819

Gnomad4 NFE AF: 0.863

Gnomad4 OTH AF: 0.847

Alfa AF: 0.850 Hom.: 8934

Bravo AF: 0.831

Asia WGS AF: 0.788 AC: 2740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.0
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1487683; hg19: chr11-104388714;