rs10488793

Variant names:

• chr11-29774697-A-T
• rs10488793
• ENST00000528553.2:n.27-131877T>A

Variant summary

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

The ENST00000528553.2(LINC02755):​n.27-131877T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0137 in 152,162 control chromosomes in the GnomAD database, including 114 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 0.014 (114 hom., cov: 32)
• Consequence: LINC02755 ENST00000528553.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.12

Genes affected

LINC02755 (HGNC:54275): (long intergenic non-protein coding RNA 2755)

ENSG00000254734 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0949 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
LINC02755	ENST00000528553.2	n.27-131877T>A		intron_variant	Intron 1 of 6	3
ENSG00000254734	ENST00000530249.1	n.233-29794A>T		intron_variant	Intron 1 of 2	4
LINC02755	ENST00000657392.1	n.51-131877T>A		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.0137 AC: 2081 AN: 152044 Hom.: 111 Cov.: 32

Gnomad AFR AF: 0.00317

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0983

Gnomad ASJ AF: 0.00288

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0232

Gnomad FIN AF: 0.0112

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00256

Gnomad OTH AF: 0.0139

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

GnomAD4 genome AF: 0.0137 AC: 2091 AN: 152162 Hom.: 114 Cov.: 32 AF XY: 0.0160 AC XY: 1190 AN XY: 74412

Gnomad4 AFR AF: 0.00316

Gnomad4 AMR AF: 0.0990

Gnomad4 ASJ AF: 0.00288

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0228

Gnomad4 FIN AF: 0.0112

Gnomad4 NFE AF: 0.00256

Gnomad4 OTH AF: 0.0137

Alfa AF: 0.0100 Hom.: 16

Bravo AF: 0.0215

Asia WGS AF: 0.0160 AC: 54 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.0
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10488793; hg19: chr11-29796244;