chr6-31507419-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005931.5(MICB):c.912G>C(p.Gln304His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000342 in 1,461,880 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.912G>C | p.Gln304His | missense_variant | 5/6 | ENST00000252229.7 | |
MICB | NM_001289160.2 | c.816G>C | p.Gln272His | missense_variant | 5/6 | ||
MICB | NM_001289161.2 | c.783G>C | p.Gln261His | missense_variant | 5/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MICB | ENST00000252229.7 | c.912G>C | p.Gln304His | missense_variant | 5/6 | 1 | NM_005931.5 | P1 | |
MICB | ENST00000399150.7 | c.783G>C | p.Gln261His | missense_variant | 5/6 | 1 | |||
MICB | ENST00000538442.5 | c.816G>C | p.Gln272His | missense_variant | 5/6 | 2 | |||
MICB | ENST00000494577.1 | n.795G>C | non_coding_transcript_exon_variant | 3/3 | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249558Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135394
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461880Hom.: 0 Cov.: 35 AF XY: 0.00000275 AC XY: 2AN XY: 727244
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 15, 2023 | The c.912G>C (p.Q304H) alteration is located in exon 5 (coding exon 5) of the MICB gene. This alteration results from a G to C substitution at nucleotide position 912, causing the glutamine (Q) at amino acid position 304 to be replaced by a histidine (H). 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