rs35690712
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_006979.3(SLC39A7):āc.370G>Cā(p.Gly124Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.033 in 1,612,224 control chromosomes in the GnomAD database, including 1,244 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 (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Synonymous variant affecting the same amino acid position (i.e. G124G) has been classified as Uncertain significance.
Frequency
Consequence
NM_006979.3 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 |
---|---|---|---|---|---|---|---|
SLC39A7 | NM_006979.3 | c.370G>C | p.Gly124Arg | missense_variant | 1/7 | ENST00000374677.8 | |
SLC39A7 | NM_001077516.2 | c.370G>C | p.Gly124Arg | missense_variant | 2/8 | ||
SLC39A7 | NM_001288777.2 | c.53-146G>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC39A7 | ENST00000374677.8 | c.370G>C | p.Gly124Arg | missense_variant | 1/7 | 1 | NM_006979.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0292 AC: 4438AN: 152126Hom.: 121 Cov.: 32
GnomAD3 exomes AF: 0.0354 AC: 8828AN: 249126Hom.: 283 AF XY: 0.0376 AC XY: 5087AN XY: 135154
GnomAD4 exome AF: 0.0334 AC: 48729AN: 1459980Hom.: 1124 Cov.: 33 AF XY: 0.0348 AC XY: 25260AN XY: 725938
GnomAD4 genome ? AF: 0.0291 AC: 4436AN: 152244Hom.: 120 Cov.: 32 AF XY: 0.0284 AC XY: 2113AN XY: 74426
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at