rs17439299

Positions:

• chr11-15599040-A-G

Variant summary

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

The NR_169502.1(LINC02751):​n.587+13238A>G 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 0.108 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: LINC02751 NR_169502.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.519

Genes affected

(HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC02751	NR_169502.1	n.587+13238A>G		intron_variant, non_coding_transcript_variant
LOC105376568	XR_931075.3	n.482+23265T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000657022.2	n.143+23265T>C		intron_variant, non_coding_transcript_variant
LINC02751	ENST00000659618.1	n.506-4892A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0906

Gnomad4 AMR AF: 0.0749

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.0709

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.235

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.0945

Alfa AF: 0.0983 Hom.: 363

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17439299; hg19: chr11-15620586;