chr19-10287066-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_001544.5(ICAM4):c.54G>A(p.Pro18Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000139 in 1,581,988 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Consequence
NM_001544.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ICAM4 | NM_001544.5 | c.54G>A | p.Pro18Pro | synonymous_variant | Exon 1 of 3 | ENST00000380770.5 | NP_001535.1 | |
ICAM4 | NM_001039132.3 | c.54G>A | p.Pro18Pro | synonymous_variant | Exon 1 of 3 | NP_001034221.1 | ||
ICAM4-AS1 | NR_186335.1 | n.1954C>T | non_coding_transcript_exon_variant | Exon 1 of 1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ICAM4 | ENST00000380770.5 | c.54G>A | p.Pro18Pro | synonymous_variant | Exon 1 of 3 | 1 | NM_001544.5 | ENSP00000370147.2 | ||
ICAM4 | ENST00000340992.4 | c.54G>A | p.Pro18Pro | synonymous_variant | Exon 1 of 3 | 1 | ENSP00000342114.3 | |||
ICAM4 | ENST00000393717.2 | c.54G>A | p.Pro18Pro | synonymous_variant | Exon 1 of 2 | 2 | ENSP00000377320.1 | |||
ICAM4-AS1 | ENST00000589379.1 | n.1954C>T | non_coding_transcript_exon_variant | Exon 1 of 1 | 6 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152180Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000147 AC: 21AN: 1429808Hom.: 0 Cov.: 31 AF XY: 0.0000155 AC XY: 11AN XY: 707478
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152180Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74348
ClinVar
Submissions by phenotype
not provided Uncertain:1
The ICAM4 p.Pro18Pro variant was not identified in the literature nor was it identified in ClinVar, Cosmic, or LOVD 3.0. The variant was identified in dbSNP (ID: rs762283483) and in control databases in 4 of 255224 chromosomes at a frequency of 0.000016 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: East Asian in 1 of 18598 chromosomes (freq: 0.000054) and European (non-Finnish) in 3 of 116222 chromosomes (freq: 0.000026), but not in the African, Latino, Ashkenazi Jewish, European (Finnish), Other, and South Asian populations. The p. Pro18Pro variant is not expected to have clinical significance because it does not result in a change of amino acid and is not located in a known consensus splice site. However, 3 of 4 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) predict a greater than 10% difference in splicing and the creation of a new 3' splice site. However, this information is not predictive enough to assume pathogenicity. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at