chr4-41990684-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006345.4(SLC30A9):c.33C>G(p.His11Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,610,034 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006345.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC30A9 | NM_006345.4 | c.33C>G | p.His11Gln | missense_variant | 1/18 | ENST00000264451.12 | |
SLC30A9 | XM_047449525.1 | c.33C>G | p.His11Gln | missense_variant | 1/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC30A9 | ENST00000264451.12 | c.33C>G | p.His11Gln | missense_variant | 1/18 | 1 | NM_006345.4 | P1 | |
SLC30A9 | ENST00000510460.1 | n.158C>G | non_coding_transcript_exon_variant | 1/4 | 2 | ||||
SLC30A9 | ENST00000513699.5 | c.33C>G | p.His11Gln | missense_variant, NMD_transcript_variant | 1/19 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152250Hom.: 0 Cov.: 33
GnomAD4 exome AF: 6.86e-7 AC: 1AN: 1457666Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 724584
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152368Hom.: 0 Cov.: 33 AF XY: 0.0000268 AC XY: 2AN XY: 74514
ClinVar
Submissions by phenotype
See cases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein | Apr 05, 2020 | ACMG classification criteria: PM2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at