6-109444275-C-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_022765.4(MICAL1):c.3120G>T(p.Leu1040Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00008 in 1,613,476 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_022765.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MICAL1 | NM_022765.4 | c.3120G>T | p.Leu1040Phe | missense_variant | 25/25 | ENST00000358807.8 | NP_073602.3 | |
MICAL1 | NM_001286613.2 | c.3177G>T | p.Leu1059Phe | missense_variant | 25/25 | NP_001273542.1 | ||
MICAL1 | NM_001159291.2 | c.2862G>T | p.Leu954Phe | missense_variant | 24/24 | NP_001152763.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MICAL1 | ENST00000358807.8 | c.3120G>T | p.Leu1040Phe | missense_variant | 25/25 | 1 | NM_022765.4 | ENSP00000351664 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152174Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000223 AC: 56AN: 250944Hom.: 0 AF XY: 0.000169 AC XY: 23AN XY: 135820
GnomAD4 exome AF: 0.0000814 AC: 119AN: 1461302Hom.: 0 Cov.: 33 AF XY: 0.0000743 AC XY: 54AN XY: 726966
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152174Hom.: 1 Cov.: 33 AF XY: 0.0000807 AC XY: 6AN XY: 74340
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 11, 2021 | The c.3120G>T (p.L1040F) alteration is located in exon 25 (coding exon 24) of the MICAL1 gene. This alteration results from a G to T substitution at nucleotide position 3120, causing the leucine (L) at amino acid position 1040 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 21, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at