chr8-22404734-G-A
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_015359.6(SLC39A14):c.24G>A(p.Pro8=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00947 in 1,613,480 control chromosomes in the GnomAD database, including 98 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. P8P) has been classified as Likely benign.
Frequency
Consequence
NM_015359.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC39A14 | NM_001128431.4 | c.24G>A | p.Pro8= | synonymous_variant | 2/9 | ENST00000381237.6 | |
SLC39A14 | NM_015359.6 | c.24G>A | p.Pro8= | synonymous_variant | 2/9 | ENST00000359741.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC39A14 | ENST00000359741.10 | c.24G>A | p.Pro8= | synonymous_variant | 2/9 | 2 | NM_015359.6 | A2 | |
SLC39A14 | ENST00000381237.6 | c.24G>A | p.Pro8= | synonymous_variant | 2/9 | 1 | NM_001128431.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00760 AC: 1155AN: 151884Hom.: 9 Cov.: 32
GnomAD3 exomes AF: 0.00699 AC: 1749AN: 250074Hom.: 9 AF XY: 0.00731 AC XY: 989AN XY: 135368
GnomAD4 exome AF: 0.00966 AC: 14121AN: 1461480Hom.: 89 Cov.: 35 AF XY: 0.00964 AC XY: 7009AN XY: 727068
GnomAD4 genome ? AF: 0.00760 AC: 1155AN: 152000Hom.: 9 Cov.: 32 AF XY: 0.00698 AC XY: 519AN XY: 74330
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2024 | SLC39A14: BP4, BP7, BS1, BS2 - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at