chr19-10285007-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000201.3(ICAM1):āc.1405A>Gā(p.Lys469Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.423 in 1,613,062 control chromosomes in the GnomAD database, including 148,506 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). 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.1405A>G | p.Lys469Glu | missense_variant | 6/7 | ENST00000264832.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ICAM1 | ENST00000264832.8 | c.1405A>G | p.Lys469Glu | missense_variant | 6/7 | 1 | NM_000201.3 | P1 | |
LIMASI | ENST00000592893.1 | n.102T>C | non_coding_transcript_exon_variant | 1/3 | 3 | ||||
ICAM1 | ENST00000423829.2 | c.739A>G | p.Lys247Glu | missense_variant | 4/5 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.372 AC: 56534AN: 151900Hom.: 11683 Cov.: 32
GnomAD3 exomes AF: 0.438 AC: 109733AN: 250628Hom.: 25472 AF XY: 0.442 AC XY: 59930AN XY: 135520
GnomAD4 exome AF: 0.429 AC: 626242AN: 1461044Hom.: 136824 Cov.: 53 AF XY: 0.431 AC XY: 313016AN XY: 726776
GnomAD4 genome ? AF: 0.372 AC: 56537AN: 152018Hom.: 11682 Cov.: 32 AF XY: 0.376 AC XY: 27951AN XY: 74290
ClinVar
Submissions by phenotype
ICAM1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 17, 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