4-123028401-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_145207.3(AFG2A):c.2079+6G>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_145207.3 splice_region, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SPATA5 | ENST00000274008.5 | c.2079+6G>C | splice_region_variant, intron_variant | 1 | NM_145207.3 | ENSP00000274008.3 | ||||
SPATA5 | ENST00000422835.2 | n.2121+6G>C | splice_region_variant, intron_variant | 1 | ||||||
SPATA5 | ENST00000675612.1 | c.2148+6G>C | splice_region_variant, intron_variant | ENSP00000502453.1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 152124Hom.: 0 Cov.: 32 FAILED QC
GnomAD4 exome Cov.: 38
GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 152124Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74306
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at