chr4-682187-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_032219.4(SLC49A3):c.1451C>T(p.Pro484Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000244 in 1,362,656 control chromosomes in the GnomAD database, including 1 homozygotes. 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC49A3 | NM_032219.4 | c.1451C>T | p.Pro484Leu | missense_variant | 10/10 | ENST00000322224.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC49A3 | ENST00000322224.9 | c.1451C>T | p.Pro484Leu | missense_variant | 10/10 | 1 | NM_032219.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000204 AC: 31AN: 152110Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000419 AC: 28AN: 66758Hom.: 0 AF XY: 0.000499 AC XY: 19AN XY: 38100
GnomAD4 exome AF: 0.000249 AC: 302AN: 1210546Hom.: 1 Cov.: 31 AF XY: 0.000245 AC XY: 144AN XY: 588314
GnomAD4 genome ? AF: 0.000204 AC: 31AN: 152110Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74292
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 03, 2024 | The c.1451C>T (p.P484L) alteration is located in exon 10 (coding exon 10) of the MFSD7 gene. This alteration results from a C to T substitution at nucleotide position 1451, causing the proline (P) at amino acid position 484 to be replaced by a leucine (L). 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