rs1393275

chr11-115784716-T-C

Variant summary

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

The ENST00000539305.1(LINC02698):n.164-58020T>C 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 0.114 in 152,250 control chromosomes in the GnomAD database, including 1,626 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 (1626 hom., cov: 32)
• Consequence: LINC02698 ENST00000539305.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

Genes affected

LINC02698 (HGNC:54212): (long intergenic non-protein coding RNA 2698)

LOC107987165 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.245 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02698	XR_001748394.3	n.468+107935T>C		intron_variant, non_coding_transcript_variant
LOC107987165	XR_001748395.2	n.560+4382A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02698	ENST00000539305.1	n.164-58020T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17222 AN: 152132 Hom.: 1604 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0804

Gnomad ASJ AF: 0.0639

Gnomad EAS AF: 0.0731

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.0174

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0594

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.114 AC: 17290 AN: 152250 Hom.: 1626 Cov.: 32 AF XY: 0.110 AC XY: 8220 AN XY: 74454

Gnomad4 AFR AF: 0.249

Gnomad4 AMR AF: 0.0803

Gnomad4 ASJ AF: 0.0639

Gnomad4 EAS AF: 0.0726

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.0174

Gnomad4 NFE AF: 0.0594

Gnomad4 OTH AF: 0.107

Alfa AF: 0.0733 Hom.: 656

Bravo AF: 0.121

Asia WGS AF: 0.112 AC: 392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.62
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1393275; hg19: chr11-115655434;