rs1051788
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005931.5(MICB):c.406G>A(p.Asp136Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 1,613,810 control chromosomes in the GnomAD database, including 76,980 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D136H) has been classified as Likely benign.
Frequency
Consequence
NM_005931.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MICB | NM_005931.5 | c.406G>A | p.Asp136Asn | missense_variant | 3/6 | ENST00000252229.7 | |
MICB | NM_001289160.2 | c.310G>A | p.Asp104Asn | missense_variant | 3/6 | ||
MICB | NM_001289161.2 | c.326-49G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MICB | ENST00000252229.7 | c.406G>A | p.Asp136Asn | missense_variant | 3/6 | 1 | NM_005931.5 | P1 | |
MICB | ENST00000399150.7 | c.326-49G>A | intron_variant | 1 | |||||
MICB | ENST00000538442.5 | c.310G>A | p.Asp104Asn | missense_variant | 3/6 | 2 | |||
MICB | ENST00000494577.1 | n.289G>A | non_coding_transcript_exon_variant | 1/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.314 AC: 47742AN: 151852Hom.: 7759 Cov.: 32
GnomAD3 exomes AF: 0.293 AC: 72991AN: 249430Hom.: 11442 AF XY: 0.299 AC XY: 40503AN XY: 135346
GnomAD4 exome AF: 0.304 AC: 444598AN: 1461840Hom.: 69212 Cov.: 56 AF XY: 0.306 AC XY: 222666AN XY: 727206
GnomAD4 genome ? AF: 0.314 AC: 47784AN: 151970Hom.: 7768 Cov.: 32 AF XY: 0.310 AC XY: 22997AN XY: 74296
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at