rs1393275

Variant names:

• chr11-115784716-T-C
• rs1393275
• ENST00000539305.2:n.682-58020T>C

Variant summary

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

The ENST00000539305.2(LINC02698):​n.682-58020T>C variant causes a intron 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 ENST00000539305.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 2 publications found

Genes affected

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

ENSG00000302547 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000539305.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02698	ENST00000539305.2	TSL:4	n.682-58020T>C		intron	N/A
	ENSG00000302547	ENST00000787773.1		n.369+4382A>G		intron	N/A
	ENSG00000302547	ENST00000787774.1		n.336+4382A>G		intron	N/A

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

African (AFR) AF: 0.249 AC: 10347 AN: 41520

American (AMR) AF: 0.0803 AC: 1229 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0639 AC: 222 AN: 3472

East Asian (EAS) AF: 0.0726 AC: 376 AN: 5176

South Asian (SAS) AF: 0.129 AC: 622 AN: 4820

European-Finnish (FIN) AF: 0.0174 AC: 185 AN: 10620

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0594 AC: 4039 AN: 68018

Other (OTH) AF: 0.107 AC: 226 AN: 2114

Alfa AF: 0.0775 Hom.: 1209

Bravo AF: 0.121

Asia WGS AF: 0.112 AC: 392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.62
DANN	Benign	0.36
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1393275; hg19: chr11-115655434;