6-31507075-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005931.5(MICB):c.667G>A(p.Val223Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000192 in 1,613,868 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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MICB | NM_005931.5 | c.667G>A | p.Val223Met | missense_variant | 4/6 | ENST00000252229.7 | |
MICB | NM_001289160.2 | c.571G>A | p.Val191Met | missense_variant | 4/6 | ||
MICB | NM_001289161.2 | c.538G>A | p.Val180Met | missense_variant | 4/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MICB | ENST00000252229.7 | c.667G>A | p.Val223Met | missense_variant | 4/6 | 1 | NM_005931.5 | P1 | |
MICB | ENST00000399150.7 | c.538G>A | p.Val180Met | missense_variant | 4/6 | 1 | |||
MICB | ENST00000538442.5 | c.571G>A | p.Val191Met | missense_variant | 4/6 | 2 | |||
MICB | ENST00000494577.1 | n.550G>A | non_coding_transcript_exon_variant | 2/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000281 AC: 7AN: 249300Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135262
GnomAD4 exome AF: 0.0000205 AC: 30AN: 1461678Hom.: 0 Cov.: 34 AF XY: 0.0000234 AC XY: 17AN XY: 727150
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152190Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 06, 2022 | The c.667G>A (p.V223M) alteration is located in exon 4 (coding exon 4) of the MICB gene. This alteration results from a G to A substitution at nucleotide position 667, causing the valine (V) at amino acid position 223 to be replaced by a methionine (M). 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