16-88654687-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_002461.3(MVD):c.1013+5G>A variant causes a splice region, intron change. The variant allele was found at a frequency of 0.0000069 in 1,594,012 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_002461.3 splice_region, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MVD | NM_002461.3 | c.1013+5G>A | splice_region_variant, intron_variant | Intron 8 of 9 | ENST00000301012.8 | NP_002452.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MVD | ENST00000301012.8 | c.1013+5G>A | splice_region_variant, intron_variant | Intron 8 of 9 | 1 | NM_002461.3 | ENSP00000301012.3 | |||
MVD | ENST00000565149.5 | n.1572+5G>A | splice_region_variant, intron_variant | Intron 4 of 5 | 1 | |||||
MVD | ENST00000561895.1 | n.294+5G>A | splice_region_variant, intron_variant | Intron 1 of 2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152262Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.00000434 AC: 1AN: 230640Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 126094
GnomAD4 exome AF: 0.00000416 AC: 6AN: 1441750Hom.: 0 Cov.: 31 AF XY: 0.00000558 AC XY: 4AN XY: 717366
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152262Hom.: 0 Cov.: 34 AF XY: 0.0000403 AC XY: 3AN XY: 74386
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at