rs10488792

Variant names:

• chr11-29774838-G-A
• rs10488792
• ENST00000528553.2:n.27-132018C>T

Your query was ambiguous. Multiple possible variants found:

• chr11-29774838-G-A
• chr11-29774838-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000528553.2(LINC02755):​n.27-132018C>T 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 152,090 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: 0.214
• Publications: 1 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0947 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.27-132018C>T		intron_variant	Intron 1 of 6	3
ENSG00000254734	ENST00000530249.1	n.233-29653G>A		intron_variant	Intron 1 of 2	4
LINC02755	ENST00000657392.1	n.51-132018C>T		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.0137 AC: 2081 AN: 151972 Hom.: 111 Cov.: 32

Gnomad AFR AF: 0.00319

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0982

Gnomad ASJ AF: 0.00289

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0233

Gnomad FIN AF: 0.0112

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00257

Gnomad OTH AF: 0.0143

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

GnomAD4 genome AF: 0.0137 AC: 2091 AN: 152090 Hom.: 114 Cov.: 32 AF XY: 0.0160 AC XY: 1189 AN XY: 74330

African (AFR) AF: 0.00318 AC: 132 AN: 41498

American (AMR) AF: 0.0988 AC: 1508 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.00289 AC: 10 AN: 3466

East Asian (EAS) AF: 0.00136 AC: 7 AN: 5166

South Asian (SAS) AF: 0.0229 AC: 110 AN: 4812

European-Finnish (FIN) AF: 0.0112 AC: 119 AN: 10578

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

European-Non Finnish (NFE) AF: 0.00257 AC: 175 AN: 67990

Other (OTH) AF: 0.0142 AC: 30 AN: 2114

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	-0.85
CADD	Benign	2.6
DANN	Benign	0.67
PhyloP100		0.21
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: rs10488792; hg19: chr11-29796385;