chr6-31509818-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_005931.5(MICB):c.1061T>C(p.Val354Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000787 in 1,613,430 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 | UniProt |
---|---|---|---|---|---|---|---|
MICB | NM_005931.5 | c.1061T>C | p.Val354Ala | missense_variant | 6/6 | ENST00000252229.7 | |
MICB | NM_001289160.2 | c.965T>C | p.Val322Ala | missense_variant | 6/6 | ||
MICB | NM_001289161.2 | c.932T>C | p.Val311Ala | missense_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MICB | ENST00000252229.7 | c.1061T>C | p.Val354Ala | missense_variant | 6/6 | 1 | NM_005931.5 | P1 | |
MICB | ENST00000399150.7 | c.932T>C | p.Val311Ala | missense_variant | 6/6 | 1 | |||
MICB | ENST00000538442.5 | c.965T>C | p.Val322Ala | missense_variant | 6/6 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000789 AC: 12AN: 152130Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000117 AC: 29AN: 248458Hom.: 0 AF XY: 0.000133 AC XY: 18AN XY: 134840
GnomAD4 exome AF: 0.0000787 AC: 115AN: 1461182Hom.: 0 Cov.: 34 AF XY: 0.0000757 AC XY: 55AN XY: 726920
GnomAD4 genome ? AF: 0.0000788 AC: 12AN: 152248Hom.: 0 Cov.: 32 AF XY: 0.0000941 AC XY: 7AN XY: 74424
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 27, 2022 | The c.1061T>C (p.V354A) alteration is located in exon 6 (coding exon 6) of the MICB gene. This alteration results from a T to C substitution at nucleotide position 1061, causing the valine (V) at amino acid position 354 to be replaced by an alanine (A). 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