19-40775761-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_006533.4(MIA):c.137C>T(p.Ser46Phe) variant causes a missense change. The variant allele was found at a frequency of 0.000026 in 1,614,160 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006533.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MIA | NM_006533.4 | c.137C>T | p.Ser46Phe | missense_variant | Exon 2 of 4 | ENST00000263369.4 | NP_006524.1 | |
MIA | NM_001202553.2 | c.137C>T | p.Ser46Phe | missense_variant | Exon 3 of 5 | NP_001189482.1 | ||
MIA-RAB4B | NR_037775.1 | n.143C>T | non_coding_transcript_exon_variant | Exon 2 of 10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MIA | ENST00000263369.4 | c.137C>T | p.Ser46Phe | missense_variant | Exon 2 of 4 | 1 | NM_006533.4 | ENSP00000263369.2 | ||
MIA-RAB4B | ENST00000600729.2 | n.137C>T | non_coding_transcript_exon_variant | Exon 3 of 11 | 5 | ENSP00000472384.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251442Hom.: 0 AF XY: 0.0000883 AC XY: 12AN XY: 135892
GnomAD4 exome AF: 0.0000274 AC: 40AN: 1461884Hom.: 1 Cov.: 31 AF XY: 0.0000358 AC XY: 26AN XY: 727244
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152276Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74456
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.137C>T (p.S46F) alteration is located in exon 2 (coding exon 2) of the MIA gene. This alteration results from a C to T substitution at nucleotide position 137, causing the serine (S) at amino acid position 46 to be replaced by a phenylalanine (F). 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