rs10488793

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

Genes affected

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

ENSG00000254734 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.00316 AC: 131 AN: 41506

American (AMR) AF: 0.0990 AC: 1511 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.00288 AC: 10 AN: 3468

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5184

South Asian (SAS) AF: 0.0228 AC: 110 AN: 4814

European-Finnish (FIN) AF: 0.0112 AC: 119 AN: 10606

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00256 AC: 174 AN: 68006

Other (OTH) AF: 0.0137 AC: 29 AN: 2110

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
PhyloP100		1.1
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10488793; hg19: chr11-29796244;