chr11-63659256-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_015459.5(ATL3):c.47-4A>G variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000372 in 1,613,068 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 predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_015459.5 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATL3 | NM_015459.5 | c.47-4A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000398868.8 | |||
ATL3 | NM_001290048.2 | c.-8-4A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
ATL3 | XM_006718493.2 | c.47-4A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
ATL3 | XM_047426725.1 | c.203-4A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATL3 | ENST00000398868.8 | c.47-4A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_015459.5 | ||||
ATL3 | ENST00000538786.1 | c.-8-4A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 2 | P1 | ||||
ATL3 | ENST00000540699.1 | c.203-4A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 3 | |||||
ATL3 | ENST00000535789.1 | n.614-4A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152150Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1460918Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 726768
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152150Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74330
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at