chr6-33201405-T-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_006979.3(SLC39A7):āc.160T>Cā(p.Phe54Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0114 in 1,613,992 control chromosomes in the GnomAD database, including 149 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_006979.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC39A7 | NM_006979.3 | c.160T>C | p.Phe54Leu | missense_variant | 1/7 | ENST00000374677.8 | NP_008910.2 | |
SLC39A7 | NM_001077516.2 | c.160T>C | p.Phe54Leu | missense_variant | 2/8 | NP_001070984.1 | ||
SLC39A7 | NM_001288777.2 | c.52+17T>C | intron_variant | NP_001275706.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC39A7 | ENST00000374677.8 | c.160T>C | p.Phe54Leu | missense_variant | 1/7 | 1 | NM_006979.3 | ENSP00000363809 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00815 AC: 1239AN: 152032Hom.: 6 Cov.: 32
GnomAD3 exomes AF: 0.00668 AC: 1666AN: 249574Hom.: 8 AF XY: 0.00649 AC XY: 879AN XY: 135404
GnomAD4 exome AF: 0.0117 AC: 17144AN: 1461842Hom.: 143 Cov.: 32 AF XY: 0.0112 AC XY: 8139AN XY: 727224
GnomAD4 genome AF: 0.00814 AC: 1238AN: 152150Hom.: 6 Cov.: 32 AF XY: 0.00773 AC XY: 575AN XY: 74376
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2024 | SLC39A7: BS1, BS2 - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 01, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at