chr4-683270-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_032219.4(SLC49A3):c.1091C>T(p.Ala364Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000154 in 1,612,702 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 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.1091C>T | p.Ala364Val | missense_variant | 8/10 | ENST00000322224.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC49A3 | ENST00000322224.9 | c.1091C>T | p.Ala364Val | missense_variant | 8/10 | 1 | NM_032219.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000855 AC: 13AN: 152066Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000141 AC: 35AN: 248894Hom.: 0 AF XY: 0.000141 AC XY: 19AN XY: 135168
GnomAD4 exome AF: 0.000161 AC: 235AN: 1460518Hom.: 0 Cov.: 33 AF XY: 0.000156 AC XY: 113AN XY: 726580
GnomAD4 genome ? AF: 0.0000854 AC: 13AN: 152184Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74416
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 25, 2023 | The c.1091C>T (p.A364V) alteration is located in exon 8 (coding exon 8) of the MFSD7 gene. This alteration results from a C to T substitution at nucleotide position 1091, causing the alanine (A) at amino acid position 364 to be replaced by a valine (V). 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