rs1054986
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000585759.1(SLC14A2-AS1):n.245-1581A>G 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 0.355 in 152,070 control chromosomes in the GnomAD database, including 11,581 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
ENST00000585759.1 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 |
---|---|---|---|---|---|---|---|
SLC14A2-AS1 | XR_007066352.1 | n.9038-1581A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC14A2-AS1 | ENST00000585759.1 | n.245-1581A>G | intron_variant, non_coding_transcript_variant | 3 | |||||
SLC14A2 | ENST00000586448.5 | c.-124-44934T>C | intron_variant | 2 | P1 | ||||
SLC14A2-AS1 | ENST00000592286.1 | n.415A>G | non_coding_transcript_exon_variant | 2/2 | 4 | ||||
SLC14A2-AS1 | ENST00000592899.1 | n.234A>G | non_coding_transcript_exon_variant | 3/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.355 AC: 53982AN: 151952Hom.: 11582 Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0AC: 0AN: 0Hom.: 0 Cov.: 0AC XY: 0AN XY: 0
GnomAD4 genome ? AF: 0.355 AC: 53971AN: 152070Hom.: 11581 Cov.: 32 AF XY: 0.355 AC XY: 26365AN XY: 74326
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at