chr4-683649-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_032219.4(SLC49A3):c.953G>C(p.Gly318Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000109 in 1,612,286 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032219.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC49A3 | NM_032219.4 | c.953G>C | p.Gly318Ala | missense_variant | 7/10 | ENST00000322224.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC49A3 | ENST00000322224.9 | c.953G>C | p.Gly318Ala | missense_variant | 7/10 | 1 | NM_032219.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000920 AC: 14AN: 152170Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000729 AC: 18AN: 246924Hom.: 0 AF XY: 0.0000970 AC XY: 13AN XY: 134020
GnomAD4 exome AF: 0.000111 AC: 162AN: 1460116Hom.: 0 Cov.: 35 AF XY: 0.000120 AC XY: 87AN XY: 726254
GnomAD4 genome ? AF: 0.0000920 AC: 14AN: 152170Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74328
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 06, 2022 | The c.953G>C (p.G318A) alteration is located in exon 7 (coding exon 7) of the MFSD7 gene. This alteration results from a G to C substitution at nucleotide position 953, causing the glycine (G) at amino acid position 318 to be replaced by an alanine (A). 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