8-22404670-G-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_015359.6(SLC39A14):c.-15-26G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 1,590,420 control chromosomes in the GnomAD database, including 38,048 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.28 ( 7759 hom., cov: 31)
Exomes 𝑓: 0.20 ( 30289 hom. )
Consequence
SLC39A14
NM_015359.6 intron
NM_015359.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.128
Genes affected
SLC39A14 (HGNC:20858): (solute carrier family 39 member 14) This gene encodes a member of the the SLC39A family of divalent metal transporters that mediates the cellular uptake of manganese, zinc, iron, and cadmium. The encoded protein contains eight transmembrane domains, a histidine-rich motif, and a metalloprotease motif, and is expressed on the plasma membrane and the endocytic vesicle membrane. It is an important transporter of nontransferrin-bound iron and a critical regulator of manganese homeostasis. Naturally occurring mutations in this gene are associated with neurodegeneration with brain iron accumulation and early-onset parkinsonism-dystonia with hypermanganesemia. [provided by RefSeq, May 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
?
Variant 8-22404670-G-C is Benign according to our data. Variant chr8-22404670-G-C is described in ClinVar as [Benign]. Clinvar id is 1177990.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC39A14 | NM_001128431.4 | c.-15-26G>C | intron_variant | ENST00000381237.6 | |||
SLC39A14 | NM_015359.6 | c.-15-26G>C | intron_variant | ENST00000359741.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC39A14 | ENST00000359741.10 | c.-15-26G>C | intron_variant | 2 | NM_015359.6 | A2 | |||
SLC39A14 | ENST00000381237.6 | c.-15-26G>C | intron_variant | 1 | NM_001128431.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.283 AC: 42856AN: 151686Hom.: 7746 Cov.: 31
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GnomAD3 exomes AF: 0.203 AC: 47225AN: 233048Hom.: 5777 AF XY: 0.197 AC XY: 24828AN XY: 126052
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GnomAD4 exome AF: 0.196 AC: 282415AN: 1438618Hom.: 30289 Cov.: 33 AF XY: 0.194 AC XY: 138410AN XY: 712950
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GnomAD4 genome ? AF: 0.283 AC: 42906AN: 151802Hom.: 7759 Cov.: 31 AF XY: 0.279 AC XY: 20712AN XY: 74208
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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 | GeneDx | May 15, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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