12-53999990-G-A
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000513209.1(ENSG00000273049):c.166+13980G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 608,580 control chromosomes in the GnomAD database, including 94,755 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
ENST00000513209.1 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 |
---|---|---|---|---|---|---|---|---|
HOXC-AS1 | NR_047504.1 | n.21C>T | non_coding_transcript_exon_variant | Exon 1 of 2 | ||||
HOXC9 | NM_006897.3 | c.-199G>A | upstream_gene_variant | ENST00000303450.5 | NP_008828.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.553 AC: 83416AN: 150858Hom.: 23245 Cov.: 29 show subpopulations
GnomAD4 exome AF: 0.556 AC: 254364AN: 457604Hom.: 71498 Cov.: 5 AF XY: 0.551 AC XY: 132535AN XY: 240490 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.553 AC: 83455AN: 150976Hom.: 23257 Cov.: 29 AF XY: 0.549 AC XY: 40484AN XY: 73744 show subpopulations
Age Distribution
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at