11-104517986-T-G

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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02552	ENST00000536529.5	n.423-5753A>C		intron_variant, non_coding_transcript_variant		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;