chr8-144509818-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_138431.3(MFSD3):c.485C>T(p.Ser162Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000176 in 1,539,772 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_138431.3 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MFSD3 | NM_138431.3 | c.485C>T | p.Ser162Leu | missense_variant | Exon 1 of 5 | ENST00000301327.5 | NP_612440.1 | |
MFSD3 | XM_017013005.2 | c.485C>T | p.Ser162Leu | missense_variant | Exon 1 of 4 | XP_016868494.1 | ||
MFSD3 | XM_011516806.3 | c.485C>T | p.Ser162Leu | missense_variant | Exon 1 of 5 | XP_011515108.1 | ||
MFSD3 | NR_130120.2 | n.749C>T | non_coding_transcript_exon_variant | Exon 1 of 4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MFSD3 | ENST00000301327.5 | c.485C>T | p.Ser162Leu | missense_variant | Exon 1 of 5 | 1 | NM_138431.3 | ENSP00000301327.3 | ||
MFSD3 | ENST00000526749.1 | n.200C>T | non_coding_transcript_exon_variant | Exon 1 of 2 | 2 | |||||
MFSD3 | ENST00000528047.5 | n.739C>T | non_coding_transcript_exon_variant | Exon 1 of 3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000525 AC: 8AN: 152250Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000213 AC: 3AN: 140994Hom.: 0 AF XY: 0.0000131 AC XY: 1AN XY: 76488
GnomAD4 exome AF: 0.000190 AC: 263AN: 1387522Hom.: 0 Cov.: 31 AF XY: 0.000190 AC XY: 130AN XY: 685002
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152250Hom.: 0 Cov.: 34 AF XY: 0.0000403 AC XY: 3AN XY: 74380
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.485C>T (p.S162L) alteration is located in exon 1 (coding exon 1) of the MFSD3 gene. This alteration results from a C to T substitution at nucleotide position 485, causing the serine (S) at amino acid position 162 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