chr19-10271151-A-C
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The NM_000201.3(ICAM1):c.-9A>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0118 in 1,612,170 control chromosomes in the GnomAD database, including 1,905 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_000201.3 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ICAM1 | NM_000201.3 | c.-9A>C | 5_prime_UTR_variant | Exon 1 of 7 | ENST00000264832.8 | NP_000192.2 | ||
LIMASI | XR_007067137.1 | n.131-4357T>G | intron_variant | Intron 1 of 3 | ||||
LIMASI | XR_007067138.1 | n.131-4357T>G | intron_variant | Intron 1 of 3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ICAM1 | ENST00000264832 | c.-9A>C | 5_prime_UTR_variant | Exon 1 of 7 | 1 | NM_000201.3 | ENSP00000264832.2 | |||
ICAM1 | ENST00000423829 | c.-9A>C | 5_prime_UTR_variant | Exon 1 of 5 | 2 | ENSP00000413124.2 | ||||
ICAM1 | ENST00000588645 | c.-9A>C | 5_prime_UTR_variant | Exon 1 of 4 | 2 | ENSP00000465680.1 | ||||
LIMASI | ENST00000592893.1 | n.142-10723T>G | intron_variant | Intron 1 of 2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0629 AC: 9572AN: 152100Hom.: 995 Cov.: 32
GnomAD3 exomes AF: 0.0159 AC: 3922AN: 246402Hom.: 372 AF XY: 0.0116 AC XY: 1551AN XY: 134016
GnomAD4 exome AF: 0.00647 AC: 9447AN: 1459952Hom.: 908 Cov.: 30 AF XY: 0.00547 AC XY: 3973AN XY: 726274
GnomAD4 genome AF: 0.0629 AC: 9582AN: 152218Hom.: 997 Cov.: 32 AF XY: 0.0610 AC XY: 4544AN XY: 74434
ClinVar
Submissions by phenotype
ICAM1-related disorder Benign:1
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