chr16-84009843-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001080442.3(SLC38A8):c.1249C>T(p.Leu417=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000168 in 1,613,950 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. L417L) has been classified as Likely benign.
Frequency
Consequence
NM_001080442.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC38A8 | NM_001080442.3 | c.1249C>T | p.Leu417= | synonymous_variant | 11/11 | ENST00000299709.8 | |
SLC38A8 | XM_017022946.1 | c.1249C>T | p.Leu417= | synonymous_variant | 12/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC38A8 | ENST00000299709.8 | c.1249C>T | p.Leu417= | synonymous_variant | 11/11 | 5 | NM_001080442.3 | P1 | |
SLC38A8 | ENST00000568003.1 | n.325C>T | non_coding_transcript_exon_variant | 3/3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000131 AC: 20AN: 152148Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000115 AC: 29AN: 251222Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135778
GnomAD4 exome AF: 0.000172 AC: 251AN: 1461802Hom.: 0 Cov.: 31 AF XY: 0.000161 AC XY: 117AN XY: 727208
GnomAD4 genome AF: 0.000131 AC: 20AN: 152148Hom.: 0 Cov.: 33 AF XY: 0.000175 AC XY: 13AN XY: 74310
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at