6-33201334-G-C
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP6BS1
The NM_006979.3(SLC39A7):āc.89G>Cā(p.Gly30Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000304 in 1,614,024 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_006979.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC39A7 | NM_006979.3 | c.89G>C | p.Gly30Ala | missense_variant | 1/7 | ENST00000374677.8 | NP_008910.2 | |
SLC39A7 | NM_001077516.2 | c.89G>C | p.Gly30Ala | missense_variant | 2/8 | NP_001070984.1 | ||
SLC39A7 | NM_001288777.2 | c.-3G>C | 5_prime_UTR_variant | 2/8 | NP_001275706.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC39A7 | ENST00000374677.8 | c.89G>C | p.Gly30Ala | missense_variant | 1/7 | 1 | NM_006979.3 | ENSP00000363809 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152134Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000112 AC: 28AN: 249542Hom.: 0 AF XY: 0.000133 AC XY: 18AN XY: 135408
GnomAD4 exome AF: 0.000328 AC: 479AN: 1461890Hom.: 0 Cov.: 32 AF XY: 0.000305 AC XY: 222AN XY: 727246
GnomAD4 genome AF: 0.0000789 AC: 12AN: 152134Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74322
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jul 22, 2022 | This sequence change replaces glycine, which is neutral and non-polar, with alanine, which is neutral and non-polar, at codon 30 of the SLC39A7 protein (p.Gly30Ala). This variant is present in population databases (rs759427122, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with SLC39A7-related conditions. ClinVar contains an entry for this variant (Variation ID: 1411677). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The alanine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 13, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at