3-158814005-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_022736.4(MFSD1):c.590C>G(p.Ser197Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000192 in 1,612,876 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_022736.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MFSD1 | NM_022736.4 | c.590C>G | p.Ser197Cys | missense_variant | 7/16 | ENST00000415822.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MFSD1 | ENST00000415822.8 | c.590C>G | p.Ser197Cys | missense_variant | 7/16 | 1 | NM_022736.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000198 AC: 3AN: 151804Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251212Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135774
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1461072Hom.: 0 Cov.: 30 AF XY: 0.0000165 AC XY: 12AN XY: 726824
GnomAD4 genome ? AF: 0.0000198 AC: 3AN: 151804Hom.: 0 Cov.: 32 AF XY: 0.0000270 AC XY: 2AN XY: 74118
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 10, 2022 | The c.737C>G (p.S246C) alteration is located in exon 7 (coding exon 7) of the MFSD1 gene. This alteration results from a C to G substitution at nucleotide position 737, causing the serine (S) at amino acid position 246 to be replaced by a cysteine (C). 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