rs1799969
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000201.3(ICAM1):c.721G>A(p.Gly241Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 1,613,914 control chromosomes in the GnomAD database, including 10,768 homozygotes. In-silico tool predicts 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.
Frequency
Consequence
NM_000201.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ICAM1 | NM_000201.3 | c.721G>A | p.Gly241Arg | missense_variant | 4/7 | ENST00000264832.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ICAM1 | ENST00000264832.8 | c.721G>A | p.Gly241Arg | missense_variant | 4/7 | 1 | NM_000201.3 | P1 | |
LIMASI | ENST00000592893.1 | n.141+852C>T | intron_variant, non_coding_transcript_variant | 3 | |||||
ICAM1 | ENST00000423829.2 | c.68-13G>A | splice_polypyrimidine_tract_variant, intron_variant | 2 | |||||
ICAM1 | ENST00000592686.1 | downstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0911 AC: 13842AN: 152000Hom.: 942 Cov.: 32
GnomAD3 exomes AF: 0.107 AC: 26844AN: 251270Hom.: 2108 AF XY: 0.102 AC XY: 13853AN XY: 135830
GnomAD4 exome AF: 0.107 AC: 156549AN: 1461796Hom.: 9825 Cov.: 33 AF XY: 0.105 AC XY: 76247AN XY: 727214
GnomAD4 genome AF: 0.0910 AC: 13848AN: 152118Hom.: 943 Cov.: 32 AF XY: 0.0934 AC XY: 6942AN XY: 74358
ClinVar
Submissions by phenotype
ICAM1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 18, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at