rs17439299

Variant names:

• chr11-15599040-A-G
• rs17439299
• ENST00000533082.1:n.87+23265T>C

Variant summary

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

The ENST00000533082.1(ENSG00000254789):​n.87+23265T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 152,220 control chromosomes in the GnomAD database, including 977 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 0.11 (977 hom., cov: 33)
• Consequence: ENSG00000254789 ENST00000533082.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.519
• Publications: 4 publications found

Genes affected

ENSG00000254789 (HGNC:):

LINC02751 (HGNC:54271): (long intergenic non-protein coding RNA 2751)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02751	NR_169502.1	n.587+13238A>G		intron_variant	Intron 3 of 5
LINC02751	NR_169503.1	n.505+13238A>G		intron_variant	Intron 2 of 5
LINC02751	NR_169504.1	n.506-4892A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000254789	ENST00000533082.1	n.87+23265T>C		intron_variant	Intron 1 of 1	3
ENSG00000254789	ENST00000636967.5	n.129-9790T>C		intron_variant	Intron 1 of 2	5
ENSG00000254789	ENST00000657022.3	n.175+23265T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16433 AN: 152102 Hom.: 979 Cov.: 33

Gnomad AFR AF: 0.0908

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.0750

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.0704

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.0960

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

GnomAD4 genome AF: 0.108 AC: 16436 AN: 152220 Hom.: 977 Cov.: 33 AF XY: 0.113 AC XY: 8385 AN XY: 74416

African (AFR) AF: 0.0906 AC: 3765 AN: 41536

American (AMR) AF: 0.0749 AC: 1145 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 406 AN: 3468

East Asian (EAS) AF: 0.0709 AC: 367 AN: 5174

South Asian (SAS) AF: 0.136 AC: 653 AN: 4816

European-Finnish (FIN) AF: 0.235 AC: 2489 AN: 10590

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7253 AN: 68020

Other (OTH) AF: 0.0945 AC: 200 AN: 2116

Alfa AF: 0.0977 Hom.: 807

Bravo AF: 0.0943

Asia WGS AF: 0.0980 AC: 342 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	7.7
DANN	Benign	0.80
PhyloP100		0.52
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: rs17439299; hg19: chr11-15620586;