rs1056538
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003259.4(ICAM5):c.901G>A(p.Val301Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.374 in 1,612,270 control chromosomes in the GnomAD database, including 117,960 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 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 nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_003259.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ICAM5 | NM_003259.4 | c.901G>A | p.Val301Ile | missense_variant | 4/11 | ENST00000221980.5 | NP_003250.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ICAM5 | ENST00000221980.5 | c.901G>A | p.Val301Ile | missense_variant | 4/11 | 1 | NM_003259.4 | ENSP00000221980 | P1 | |
ICAM5 | ENST00000586480.1 | c.526G>A | p.Val176Ile | missense_variant | 2/9 | 1 | ENSP00000516504 |
Frequencies
GnomAD3 genomes AF: 0.312 AC: 47491AN: 152134Hom.: 8973 Cov.: 33
GnomAD3 exomes AF: 0.385 AC: 95628AN: 248350Hom.: 20093 AF XY: 0.388 AC XY: 52238AN XY: 134788
GnomAD4 exome AF: 0.381 AC: 555902AN: 1460018Hom.: 108989 Cov.: 48 AF XY: 0.382 AC XY: 277140AN XY: 726328
GnomAD4 genome AF: 0.312 AC: 47486AN: 152252Hom.: 8971 Cov.: 33 AF XY: 0.313 AC XY: 23319AN XY: 74442
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at