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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02698	XR_001748394.3	n.468+107935T>C		intron_variant	Intron 2 of 4
LOC107987165	XR_001748395.2	n.560+4382A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02698	ENST00000539305.2	n.682-58020T>C		intron_variant	Intron 2 of 2	4
ENSG00000302547	ENST00000787773.1	n.369+4382A>G		intron_variant	Intron 2 of 2
ENSG00000302547	ENST00000787774.1	n.336+4382A>G		intron_variant	Intron 2 of 2

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 v4.3

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;