6-31505805-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_005931.5(MICB):c.259G>A(p.Glu87Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000049 in 1,613,078 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005931.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MICB | NM_005931.5 | c.259G>A | p.Glu87Lys | missense_variant | 2/6 | ENST00000252229.7 | NP_005922.2 | |
MICB | NM_001289160.2 | c.163G>A | p.Glu55Lys | missense_variant | 2/6 | NP_001276089.1 | ||
MICB | NM_001289161.2 | c.259G>A | p.Glu87Lys | missense_variant | 2/6 | NP_001276090.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MICB | ENST00000252229.7 | c.259G>A | p.Glu87Lys | missense_variant | 2/6 | 1 | NM_005931.5 | ENSP00000252229.6 | ||
MICB | ENST00000399150.7 | c.259G>A | p.Glu87Lys | missense_variant | 2/6 | 1 | ENSP00000382103.3 | |||
MICB | ENST00000538442.5 | c.163G>A | p.Glu55Lys | missense_variant | 2/6 | 2 | ENSP00000442345.1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152204Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000409 AC: 10AN: 244760Hom.: 0 AF XY: 0.0000523 AC XY: 7AN XY: 133790
GnomAD4 exome AF: 0.0000513 AC: 75AN: 1460874Hom.: 0 Cov.: 36 AF XY: 0.0000509 AC XY: 37AN XY: 726742
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152204Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74344
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 26, 2021 | The c.259G>A (p.E87K) alteration is located in exon 2 (coding exon 2) of the MICB gene. This alteration results from a G to A substitution at nucleotide position 259, causing the glutamic acid (E) at amino acid position 87 to be replaced by a lysine (K). 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