12-52206622-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NR_164127.1(LINC02874):n.560G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000113 in 1,289,772 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NR_164127.1 non_coding_transcript_exon
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LINC02874 | NR_164127.1 | n.560G>A | non_coding_transcript_exon_variant | Exon 3 of 4 | ||||
LINC02874 | NR_164130.1 | n.248G>A | non_coding_transcript_exon_variant | Exon 4 of 5 | ||||
LINC02874 | NR_164131.1 | n.151G>A | non_coding_transcript_exon_variant | Exon 3 of 4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LINC02874 | ENST00000551894.6 | n.539-443G>A | intron_variant | Intron 2 of 2 | 1 | |||||
LINC02874 | ENST00000551332.1 | n.320G>A | non_coding_transcript_exon_variant | Exon 2 of 3 | 5 | |||||
LINC02874 | ENST00000665543.1 | n.569G>A | non_coding_transcript_exon_variant | Exon 3 of 4 |
Frequencies
GnomAD3 genomes AF: 0.0000985 AC: 15AN: 152254Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000520 AC: 7AN: 134618Hom.: 0 AF XY: 0.0000409 AC XY: 3AN XY: 73314
GnomAD4 exome AF: 0.000115 AC: 131AN: 1137518Hom.: 0 Cov.: 31 AF XY: 0.000108 AC XY: 60AN XY: 558054
GnomAD4 genome AF: 0.0000985 AC: 15AN: 152254Hom.: 0 Cov.: 33 AF XY: 0.000121 AC XY: 9AN XY: 74386
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.259G>A (p.G87R) alteration is located in exon 3 (coding exon 2) of the C12orf80 gene. This alteration results from a G to A substitution at nucleotide position 259, causing the glycine (G) at amino acid position 87 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at