16-58671069-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_018231.3(SLC38A7):c.1207G>T(p.Ala403Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000871 in 1,607,792 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. A403T) 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 2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152106Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000212 AC: 5AN: 236084Hom.: 0 AF XY: 0.0000156 AC XY: 2AN XY: 128222
GnomAD4 exome AF: 0.00000687 AC: 10AN: 1455686Hom.: 0 Cov.: 32 AF XY: 0.00000553 AC XY: 4AN XY: 723858
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152106Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74290
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1207G>T (p.A403S) alteration is located in exon 10 (coding exon 8) of the SLC38A7 gene. This alteration results from a G to T substitution at nucleotide position 1207, causing the alanine (A) at amino acid position 403 to be replaced by a serine (S). 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