chr12-56234869-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_173596.3(SLC39A5):c.517G>A(p.Ala173Thr) variant causes a missense change. The variant allele was found at a frequency of 0.000336 in 1,613,658 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00040 ( 2 hom., cov: 32)
Exomes 𝑓: 0.00033 ( 3 hom. )
Consequence
SLC39A5
NM_173596.3 missense
NM_173596.3 missense
Scores
4
13
Clinical Significance
Conservation
PhyloP100: 6.58
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 -10 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0064778626).
BP6
?
Variant 12-56234869-G-A is Benign according to our data. Variant chr12-56234869-G-A is described in ClinVar as [Benign]. Clinvar id is 778446.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAd at 61 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC39A5 | NM_173596.3 | c.517G>A | p.Ala173Thr | missense_variant | 6/13 | ENST00000454355.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC39A5 | ENST00000454355.7 | c.517G>A | p.Ala173Thr | missense_variant | 6/13 | 1 | NM_173596.3 | P1 | |
SLC39A5 | ENST00000266980.8 | c.517G>A | p.Ala173Thr | missense_variant | 4/11 | 1 | P1 | ||
SLC39A5 | ENST00000436633.5 | c.430G>A | p.Ala144Thr | missense_variant | 6/7 | 5 | |||
SLC39A5 | ENST00000481103.5 | n.386G>A | non_coding_transcript_exon_variant | 4/6 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000401 AC: 61AN: 152170Hom.: 2 Cov.: 32
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GnomAD3 exomes AF: 0.00120 AC: 300AN: 250676Hom.: 2 AF XY: 0.000862 AC XY: 117AN XY: 135696
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GnomAD4 exome AF: 0.000329 AC: 481AN: 1461370Hom.: 3 Cov.: 32 AF XY: 0.000286 AC XY: 208AN XY: 727020
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GnomAD4 genome ? AF: 0.000401 AC: 61AN: 152288Hom.: 2 Cov.: 32 AF XY: 0.000376 AC XY: 28AN XY: 74458
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 29, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Uncertain
DEOGEN2
Benign
T;T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.;L
MutationTaster
Benign
D;D
PrimateAI
Benign
T
PROVEAN
Benign
N;N;N
REVEL
Benign
Sift
Benign
T;D;T
Sift4G
Benign
T;T;T
Polyphen
P;.;P
Vest4
MVP
MPC
0.36
ClinPred
T
GERP RS
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at