chr10-17981381-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001145195.2(SLC39A12):c.994G>A(p.Asp332Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00253 in 1,613,692 control chromosomes in the GnomAD database, including 97 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001145195.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC39A12 | NM_001145195.2 | c.994G>A | p.Asp332Asn | missense_variant | 6/13 | ENST00000377369.7 | |
SLC39A12 | NM_001282733.2 | c.994G>A | p.Asp332Asn | missense_variant | 6/13 | ||
SLC39A12 | NM_152725.4 | c.994G>A | p.Asp332Asn | missense_variant | 6/12 | ||
SLC39A12 | NM_001282734.2 | c.592G>A | p.Asp198Asn | missense_variant | 5/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC39A12 | ENST00000377369.7 | c.994G>A | p.Asp332Asn | missense_variant | 6/13 | 1 | NM_001145195.2 | A1 | |
SLC39A12 | ENST00000377371.3 | c.994G>A | p.Asp332Asn | missense_variant | 6/13 | 1 | P4 | ||
SLC39A12 | ENST00000377374.8 | c.994G>A | p.Asp332Asn | missense_variant | 6/12 | 2 | |||
SLC39A12 | ENST00000539911.5 | c.592G>A | p.Asp198Asn | missense_variant | 5/12 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0136 AC: 2072AN: 152074Hom.: 48 Cov.: 32
GnomAD3 exomes AF: 0.00351 AC: 881AN: 251300Hom.: 21 AF XY: 0.00248 AC XY: 337AN XY: 135814
GnomAD4 exome AF: 0.00137 AC: 2001AN: 1461500Hom.: 49 Cov.: 31 AF XY: 0.00123 AC XY: 893AN XY: 727048
GnomAD4 genome ? AF: 0.0137 AC: 2081AN: 152192Hom.: 48 Cov.: 32 AF XY: 0.0125 AC XY: 930AN XY: 74410
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at