chr19-10334150-G-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002162.5(ICAM3):c.1441+10C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.655 in 1,611,020 control chromosomes in the GnomAD database, including 346,747 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.65 ( 31891 hom., cov: 27)
Exomes 𝑓: 0.66 ( 314856 hom. )
Consequence
ICAM3
NM_002162.5 intron
NM_002162.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.19
Publications
48 publications found
Genes affected
ICAM3 (HGNC:5346): (intercellular adhesion molecule 3) The protein encoded by this gene is a member of the intercellular adhesion molecule (ICAM) family. All ICAM proteins are type I transmembrane glycoproteins, contain 2-9 immunoglobulin-like C2-type domains, and bind to the leukocyte adhesion LFA-1 protein. This protein is constitutively and abundantly expressed by all leucocytes and may be the most important ligand for LFA-1 in the initiation of the immune response. It functions not only as an adhesion molecule, but also as a potent signalling molecule. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Feb 2016]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.714 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ICAM3 | NM_002162.5 | c.1441+10C>T | intron_variant | Intron 6 of 6 | ENST00000160262.10 | NP_002153.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.647 AC: 97847AN: 151200Hom.: 31859 Cov.: 27 show subpopulations
GnomAD3 genomes
AF:
AC:
97847
AN:
151200
Hom.:
Cov.:
27
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD2 exomes AF: 0.670 AC: 167690AN: 250138 AF XY: 0.669 show subpopulations
GnomAD2 exomes
AF:
AC:
167690
AN:
250138
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.655 AC: 956493AN: 1459702Hom.: 314856 Cov.: 46 AF XY: 0.656 AC XY: 476269AN XY: 725782 show subpopulations
GnomAD4 exome
AF:
AC:
956493
AN:
1459702
Hom.:
Cov.:
46
AF XY:
AC XY:
476269
AN XY:
725782
show subpopulations
African (AFR)
AF:
AC:
20714
AN:
33454
American (AMR)
AF:
AC:
35507
AN:
44680
Ashkenazi Jewish (ASJ)
AF:
AC:
16799
AN:
26112
East Asian (EAS)
AF:
AC:
29894
AN:
39642
South Asian (SAS)
AF:
AC:
61272
AN:
86222
European-Finnish (FIN)
AF:
AC:
31426
AN:
53268
Middle Eastern (MID)
AF:
AC:
3943
AN:
5758
European-Non Finnish (NFE)
AF:
AC:
717114
AN:
1110252
Other (OTH)
AF:
AC:
39824
AN:
60314
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.482
Heterozygous variant carriers
0
17916
35832
53747
71663
89579
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
19036
38072
57108
76144
95180
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome AF: 0.647 AC: 97932AN: 151318Hom.: 31891 Cov.: 27 AF XY: 0.647 AC XY: 47807AN XY: 73888 show subpopulations
GnomAD4 genome
AF:
AC:
97932
AN:
151318
Hom.:
Cov.:
27
AF XY:
AC XY:
47807
AN XY:
73888
show subpopulations
African (AFR)
AF:
AC:
25623
AN:
41206
American (AMR)
AF:
AC:
11010
AN:
15186
Ashkenazi Jewish (ASJ)
AF:
AC:
2282
AN:
3460
East Asian (EAS)
AF:
AC:
3676
AN:
5114
South Asian (SAS)
AF:
AC:
3362
AN:
4776
European-Finnish (FIN)
AF:
AC:
6244
AN:
10474
Middle Eastern (MID)
AF:
AC:
176
AN:
294
European-Non Finnish (NFE)
AF:
AC:
43531
AN:
67804
Other (OTH)
AF:
AC:
1403
AN:
2098
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.497
Heterozygous variant carriers
0
1707
3414
5121
6828
8535
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
794
1588
2382
3176
3970
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2468
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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