ENST00000554732.5:n.222-2614C>T
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000554732.5(LINC00639):n.222-2614C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 152,102 control chromosomes in the GnomAD database, including 1,917 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
ENST00000554732.5 intron
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Benign. The variant received -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LINC00639 | NR_039982.1 | n.160-2614C>T | intron_variant | Intron 2 of 4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LINC00639 | ENST00000554732.5 | n.222-2614C>T | intron_variant | Intron 3 of 5 | 1 | |||||
LINC00639 | ENST00000553932.5 | n.155-2614C>T | intron_variant | Intron 2 of 6 | 2 | |||||
LINC00639 | ENST00000556116.2 | n.246-2614C>T | intron_variant | Intron 2 of 7 | 4 |
Frequencies
GnomAD3 genomes AF: 0.145 AC: 21972AN: 151984Hom.: 1913 Cov.: 32 show subpopulations
GnomAD4 genome AF: 0.145 AC: 22007AN: 152102Hom.: 1917 Cov.: 32 AF XY: 0.150 AC XY: 11175AN XY: 74356 show subpopulations
Age Distribution
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at