chr3-158809219-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_022736.4(MFSD1):c.481G>A(p.Ala161Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000037 in 1,594,062 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. A161V) has been classified 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 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MFSD1 | NM_022736.4 | c.481G>A | p.Ala161Thr | missense_variant | 6/16 | ENST00000415822.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MFSD1 | ENST00000415822.8 | c.481G>A | p.Ala161Thr | missense_variant | 6/16 | 1 | NM_022736.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000337 AC: 5AN: 148460Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 248130Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134166
GnomAD4 exome AF: 0.0000374 AC: 54AN: 1445602Hom.: 0 Cov.: 32 AF XY: 0.0000500 AC XY: 36AN XY: 719394
GnomAD4 genome ? AF: 0.0000337 AC: 5AN: 148460Hom.: 0 Cov.: 32 AF XY: 0.0000277 AC XY: 2AN XY: 72144
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2024 | The c.628G>A (p.A210T) alteration is located in exon 6 (coding exon 6) of the MFSD1 gene. This alteration results from a G to A substitution at nucleotide position 628, causing the alanine (A) at amino acid position 210 to be replaced by a threonine (T). 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