chr6-109444250-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_022765.4(MICAL1):c.3145C>T(p.Arg1049Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000725 in 1,613,678 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1049H) has been classified as Uncertain significance.
Frequency
Consequence
NM_022765.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MICAL1 | NM_022765.4 | c.3145C>T | p.Arg1049Cys | missense_variant | 25/25 | ENST00000358807.8 | |
MICAL1 | NM_001286613.2 | c.3202C>T | p.Arg1068Cys | missense_variant | 25/25 | ||
MICAL1 | NM_001159291.2 | c.2887C>T | p.Arg963Cys | missense_variant | 24/24 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MICAL1 | ENST00000358807.8 | c.3145C>T | p.Arg1049Cys | missense_variant | 25/25 | 1 | NM_022765.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00392 AC: 597AN: 152172Hom.: 4 Cov.: 33
GnomAD3 exomes AF: 0.000952 AC: 239AN: 250984Hom.: 3 AF XY: 0.000574 AC XY: 78AN XY: 135848
GnomAD4 exome AF: 0.000390 AC: 570AN: 1461388Hom.: 3 Cov.: 33 AF XY: 0.000331 AC XY: 241AN XY: 727000
GnomAD4 genome ? AF: 0.00394 AC: 600AN: 152290Hom.: 4 Cov.: 33 AF XY: 0.00387 AC XY: 288AN XY: 74474
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 24, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at