rs11861251
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_000632.4(ITGAM):c.1322T>A(p.Met441Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000311 in 1,608,028 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 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 variant affecting the same amino acid position, but resulting in a different missense (i.e. M441T) has been classified as Benign.
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.1322T>A | p.Met441Lys | missense_variant | 12/30 | ENST00000544665.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITGAM | ENST00000544665.9 | c.1322T>A | p.Met441Lys | missense_variant | 12/30 | 1 | NM_000632.4 | P4 | |
ITGAM | ENST00000567031.1 | c.312+1026T>A | intron_variant | 1 | |||||
ITGAM | ENST00000648685.1 | c.1322T>A | p.Met441Lys | missense_variant | 12/30 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152026Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000419 AC: 1AN: 238718Hom.: 0 AF XY: 0.00000773 AC XY: 1AN XY: 129346
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1456002Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 723634
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152026Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74228
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at