chr16-31261725-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_000632.4(ITGAM):c.62C>T(p.Thr21Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,612,770 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000632.4 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 |
---|---|---|---|---|---|---|---|
ITGAM | NM_000632.4 | c.62C>T | p.Thr21Ile | missense_variant | 2/30 | ENST00000544665.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITGAM | ENST00000544665.9 | c.62C>T | p.Thr21Ile | missense_variant | 2/30 | 1 | NM_000632.4 | P4 | |
ITGAM | ENST00000648685.1 | c.62C>T | p.Thr21Ile | missense_variant | 2/30 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000198 AC: 3AN: 151752Hom.: 0 Cov.: 29
GnomAD3 exomes AF: 0.00000806 AC: 2AN: 248116Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134568
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461018Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 726730
GnomAD4 genome ? AF: 0.0000198 AC: 3AN: 151752Hom.: 0 Cov.: 29 AF XY: 0.0000270 AC XY: 2AN XY: 74098
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Oct 22, 2023 | This sequence change replaces threonine, which is neutral and polar, with isoleucine, which is neutral and non-polar, at codon 21 of the ITGAM protein (p.Thr21Ile). This variant is present in population databases (rs373885749, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with ITGAM-related conditions. ClinVar contains an entry for this variant (Variation ID: 2192967). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at