rs646860
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000456878.1(LINC02778):n.100-15884G>A 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 0.68 in 151,850 control chromosomes in the GnomAD database, including 35,231 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
ENST00000456878.1 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 |
---|---|---|---|---|---|---|---|
LINC02778 | XR_947430.2 | n.149+17656G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LINC02778 | ENST00000456878.1 | n.100-15884G>A | intron_variant, non_coding_transcript_variant | 5 | |||||
LINC02778 | ENST00000659925.1 | n.135-215G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.680 AC: 103127AN: 151732Hom.: 35204 Cov.: 31
GnomAD4 genome ? AF: 0.680 AC: 103200AN: 151850Hom.: 35231 Cov.: 31 AF XY: 0.679 AC XY: 50351AN XY: 74206
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at