11-63629343-T-G
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_015459.5(ATL3):āc.1602A>Cā(p.Pro534Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,810 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_015459.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATL3 | NM_015459.5 | c.1602A>C | p.Pro534Pro | synonymous_variant | Exon 13 of 13 | ENST00000398868.8 | NP_056274.3 | |
ATL3 | NM_001290048.2 | c.1548A>C | p.Pro516Pro | synonymous_variant | Exon 13 of 13 | NP_001276977.1 | ||
ATL3 | XM_047426725.1 | c.1758A>C | p.Pro586Pro | synonymous_variant | Exon 14 of 14 | XP_047282681.1 | ||
ATL3 | XM_006718493.2 | c.1545A>C | p.Pro515Pro | synonymous_variant | Exon 12 of 12 | XP_006718556.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATL3 | ENST00000398868.8 | c.1602A>C | p.Pro534Pro | synonymous_variant | Exon 13 of 13 | 1 | NM_015459.5 | ENSP00000381844.3 | ||
ATL3 | ENST00000538786.1 | c.1548A>C | p.Pro516Pro | synonymous_variant | Exon 13 of 13 | 2 | ENSP00000437593.1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.00000801 AC: 2AN: 249570Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135402
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461810Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 727218
GnomAD4 genome Cov.: 31
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at