chr19-756953-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_173481.4(MISP):c.7C>T(p.Arg3Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000244 in 1,555,944 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_173481.4 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 |
---|---|---|---|---|---|---|---|---|
MISP | NM_173481.4 | c.7C>T | p.Arg3Cys | missense_variant | Exon 2 of 5 | ENST00000215582.8 | NP_775752.1 | |
MISP | XM_011527685.3 | c.7C>T | p.Arg3Cys | missense_variant | Exon 2 of 5 | XP_011525987.1 | ||
MISP | XM_011527686.3 | c.7C>T | p.Arg3Cys | missense_variant | Exon 2 of 5 | XP_011525988.1 | ||
MISP | NR_135168.2 | n.61-2956C>T | intron_variant | Intron 1 of 3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152190Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000529 AC: 1AN: 189188Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 101450
GnomAD4 exome AF: 0.0000264 AC: 37AN: 1403754Hom.: 0 Cov.: 31 AF XY: 0.0000275 AC XY: 19AN XY: 691814
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152190Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74338
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.7C>T (p.R3C) alteration is located in exon 2 (coding exon 1) of the MISP gene. This alteration results from a C to T substitution at nucleotide position 7, causing the arginine (R) at amino acid position 3 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