chr6-33202118-C-T
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7
The NM_006979.3(SLC39A7):c.627C>T(p.Ser209=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000958 in 1,460,678 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. S209S) has been classified as Benign.
Frequency
Consequence
NM_006979.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC39A7 | NM_006979.3 | c.627C>T | p.Ser209= | synonymous_variant | 3/7 | ENST00000374677.8 | |
SLC39A7 | NM_001077516.2 | c.627C>T | p.Ser209= | synonymous_variant | 4/8 | ||
SLC39A7 | NM_001288777.2 | c.252C>T | p.Ser84= | synonymous_variant | 4/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC39A7 | ENST00000374677.8 | c.627C>T | p.Ser209= | synonymous_variant | 3/7 | 1 | NM_006979.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000123 AC: 3AN: 244624Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 133896
GnomAD4 exome AF: 0.00000958 AC: 14AN: 1460678Hom.: 0 Cov.: 32 AF XY: 0.0000110 AC XY: 8AN XY: 726656
GnomAD4 genome ? Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at