chr16-58671069-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_018231.3(SLC38A7):c.1207G>A(p.Ala403Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000373 in 1,607,790 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A403S) has been classified as Uncertain significance.
Frequency
Consequence
NM_018231.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152106Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000890 AC: 21AN: 236084Hom.: 0 AF XY: 0.0000546 AC XY: 7AN XY: 128222
GnomAD4 exome AF: 0.0000378 AC: 55AN: 1455684Hom.: 0 Cov.: 32 AF XY: 0.0000276 AC XY: 20AN XY: 723856
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152106Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74290
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1207G>A (p.A403T) alteration is located in exon 10 (coding exon 8) of the SLC38A7 gene. This alteration results from a G to A substitution at nucleotide position 1207, causing the alanine (A) at amino acid position 403 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at