rs5498
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The NM_000201.3(ICAM1):c.1405A>G(p.Lys469Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 151900 control chromosomes in the gnomAD Genomes database, including 11683 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars). 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
Links
ACMG classification
Verdict is Benign. Variant got -13 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 AF XY: 0.431 AC XY: 313016AN XY: 726776
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at