rs1140700
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001177519.3(MICA):c.707T>A(p.Ile236Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,611,542 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I236T) has been classified as Benign.
Frequency
Consequence
NM_001177519.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MICA | NM_001177519.3 | c.707T>A | p.Ile236Lys | missense_variant | 4/6 | ENST00000449934.7 | |
MICA | NM_001289152.2 | c.416T>A | p.Ile139Lys | missense_variant | 4/6 | ||
MICA | NM_001289153.2 | c.416T>A | p.Ile139Lys | missense_variant | 4/6 | ||
MICA | NM_001289154.2 | c.293T>A | p.Ile98Lys | missense_variant | 4/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MICA | ENST00000449934.7 | c.707T>A | p.Ile236Lys | missense_variant | 4/6 | 1 | NM_001177519.3 | P1 | |
MICA | ENST00000616296.4 | c.416T>A | p.Ile139Lys | missense_variant | 4/6 | 5 | |||
MICA | ENST00000421350.1 | c.380T>A | p.Ile127Lys | missense_variant | 3/5 | 5 | |||
MICA | ENST00000674069.1 | c.293T>A | p.Ile98Lys | missense_variant | 4/6 |
Frequencies
GnomAD3 genomes ? AF: 0.00000660 AC: 1AN: 151532Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000906 AC: 2AN: 220848Hom.: 0 AF XY: 0.00000837 AC XY: 1AN XY: 119498
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1460010Hom.: 0 Cov.: 65 AF XY: 0.00000138 AC XY: 1AN XY: 726286
GnomAD4 genome ? AF: 0.00000660 AC: 1AN: 151532Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74034
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at