rs10488793

chr11-29774697-A-T

Variant summary

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

The ENST00000530249.1(ENSG00000254734):n.233-29794A>T 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 0.0137 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: ENST00000530249.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.12

Genes affected

(HGNC:):

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

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000530249.1	n.233-29794A>T		intron_variant, non_coding_transcript_variant		4
LINC02755	ENST00000657392.1	n.51-131877T>A		intron_variant, non_coding_transcript_variant
LINC02755	ENST00000528553.2	n.27-131877T>A		intron_variant, non_coding_transcript_variant		3

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;