12-56231415-C-T
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP7BS2
The NM_173596.3(SLC39A5):c.141C>T(p.Tyr47Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000279 in 1,614,088 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
Genomes: 𝑓 0.000026 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000028 ( 0 hom. )
Consequence
SLC39A5
NM_173596.3 synonymous
NM_173596.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.21
Genes affected
SLC39A5 (HGNC:20502): (solute carrier family 39 member 5) The protein encoded by this gene belongs to the ZIP family of zinc transporters that transport zinc into cells from outside, and play a crucial role in controlling intracellular zinc levels. Zinc is an essential cofactor for many enzymes and proteins involved in gene transcription, growth, development and differentiation. Mutations in this gene have been associated with autosomal dominant high myopia (MYP24). Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Sep 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.64).
BP7
Synonymous conserved (PhyloP=-2.21 with no splicing effect.
BS2
High AC in GnomAdExome4 at 41 AD gene.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| SLC39A5 | NM_173596.3 | c.141C>T | p.Tyr47Tyr | synonymous_variant | 4/13 | ENST00000454355.7 | NP_775867.2 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| SLC39A5 | ENST00000454355.7 | c.141C>T | p.Tyr47Tyr | synonymous_variant | 4/13 | 1 | NM_173596.3 | ENSP00000405360.2 |
Frequencies
GnomAD3 genomes 0.0000263 AC: 4AN: 152162Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251052Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135726
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GnomAD4 exome AF: 0.0000280 AC: 41AN: 1461808Hom.: 0 Cov.: 34 AF XY: 0.0000303 AC XY: 22AN XY: 727212
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GnomAD4 genome 0.0000263 AC: 4AN: 152280Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74458
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at