6-31411234-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001177519.3(MICA):c.488T>C(p.Met163Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,613,106 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
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.488T>C | p.Met163Thr | missense_variant | 3/6 | ENST00000449934.7 | |
MICA | NM_001289152.2 | c.197T>C | p.Met66Thr | missense_variant | 3/6 | ||
MICA | NM_001289153.2 | c.197T>C | p.Met66Thr | missense_variant | 3/6 | ||
MICA | NM_001289154.2 | c.84-10T>C | splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MICA | ENST00000449934.7 | c.488T>C | p.Met163Thr | missense_variant | 3/6 | 1 | NM_001177519.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000659 AC: 1AN: 151848Hom.: 0 Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461258Hom.: 0 Cov.: 61 AF XY: 0.00 AC XY: 0AN XY: 726912
GnomAD4 genome ? AF: 0.00000659 AC: 1AN: 151848Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74182
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 17, 2022 | The c.488T>C (p.M163T) alteration is located in exon 3 (coding exon 3) of the MICA gene. This alteration results from a T to C substitution at nucleotide position 488, causing the methionine (M) at amino acid position 163 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