chr2-230480845-C-T
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001080391.2(SP100):c.1600+6398C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,092 control chromosomes in the GnomAD database, with no homozygous occurrence. 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
NM_001080391.2 intron
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SP100 | NM_001080391.2 | c.1600+6398C>T | intron_variant | Intron 17 of 28 | ENST00000340126.9 | NP_001073860.1 | ||
SP100 | NM_003113.4 | c.1600+6398C>T | intron_variant | Intron 17 of 24 | NP_003104.2 | |||
SP100 | NM_001206701.2 | c.1600+6398C>T | intron_variant | Intron 17 of 22 | NP_001193630.1 | |||
LOC101928816 | XR_427235.4 | n.471+17791G>A | intron_variant | Intron 3 of 3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152092Hom.: 0 Cov.: 31 show subpopulations
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152092Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74286 show subpopulations
Age Distribution
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at