11-115784716-T-C
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
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
Consequence
ENST00000539305.1 intron, non_coding_transcript
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
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: 17222AN: 152132Hom.: 1604 Cov.: 32
GnomAD4 genome AF: 0.114 AC: 17290AN: 152250Hom.: 1626 Cov.: 32 AF XY: 0.110 AC XY: 8220AN XY: 74454
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at