rs1143679
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000632(ITGAM):c.230G>A(p.Arg77His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 152038 control chromosomes in the gnomAD Genomes database, including 974 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). 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. R77C) has been classified as Uncertain significance.
Frequency
Consequence
NM_000632 missense
Scores
Clinical Significance
Conservation
Links
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITGAM | NM_000632.4 | c.230G>A | p.Arg77His | missense_variant | 3/30 | ENST00000544665.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITGAM | ENST00000544665.9 | c.230G>A | p.Arg77His | missense_variant | 3/30 | 1 | NM_000632.4 | P4 | |
ITGAM | ENST00000648685.1 | c.230G>A | p.Arg77His | missense_variant | 3/30 | A1 |
Frequencies
GnomAD3 genomes AF: 0.108 AC: 16424AN: 152038Hom.: 974 Cov.: 31
GnomAD3 exomes AF: 0.0967 AC: 21083AN: 218036Hom.: 1170 AF XY: 0.0975 AC XY: 11570AN XY: 118716
GnomAD4 exome AF: 0.101 AC: 144937AN: 1440550Hom.: 7806 AF XY: 0.101 AC XY: 71936AN XY: 715476
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 03, 2022 | - - |
Computational scores
Source:
Splicing
Find out SpliceAI and Pangolin per-transcript scores at