chr19-10274864-A-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000201.3(ICAM1):c.167A>T(p.Lys56Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0177 in 1,614,154 control chromosomes in the GnomAD database, including 2,176 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.070 ( 1056 hom., cov: 32)
Exomes 𝑓: 0.012 ( 1120 hom. )
Consequence
ICAM1
NM_000201.3 missense
NM_000201.3 missense
Scores
18
Clinical Significance
Conservation
PhyloP100: -4.26
Genes affected
ICAM1 (HGNC:5344): (intercellular adhesion molecule 1) This gene encodes a cell surface glycoprotein which is typically expressed on endothelial cells and cells of the immune system. It binds to integrins of type CD11a / CD18, or CD11b / CD18 and is also exploited by Rhinovirus as a receptor. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.004842013).
BP6
?
Variant 19-10274864-A-T is Benign according to our data. Variant chr19-10274864-A-T is described in ClinVar as [Benign]. Clinvar id is 14661.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ICAM1 | NM_000201.3 | c.167A>T | p.Lys56Met | missense_variant | 2/7 | ENST00000264832.8 | |
LIMASI | XR_007067138.1 | n.131-8070T>A | intron_variant, non_coding_transcript_variant | ||||
LIMASI | XR_007067137.1 | n.131-8070T>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ICAM1 | ENST00000264832.8 | c.167A>T | p.Lys56Met | missense_variant | 2/7 | 1 | NM_000201.3 | P1 | |
LIMASI | ENST00000592893.1 | n.141+10104T>A | intron_variant, non_coding_transcript_variant | 3 | |||||
ICAM1 | ENST00000588645.1 | c.167A>T | p.Lys56Met | missense_variant | 2/4 | 2 | |||
ICAM1 | ENST00000423829.2 | c.67+3638A>T | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0704 AC: 10706AN: 152148Hom.: 1053 Cov.: 32
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GnomAD3 exomes AF: 0.0279 AC: 7015AN: 251466Hom.: 485 AF XY: 0.0238 AC XY: 3233AN XY: 135922
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GnomAD4 exome AF: 0.0122 AC: 17814AN: 1461888Hom.: 1120 Cov.: 32 AF XY: 0.0117 AC XY: 8506AN XY: 727246
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GnomAD4 genome ? AF: 0.0704 AC: 10727AN: 152266Hom.: 1056 Cov.: 32 AF XY: 0.0711 AC XY: 5293AN XY: 74458
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ESP6500AA
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Asia WGS
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ClinVar
Significance: Benign
Submissions summary: Benign:1Other:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
ICAM1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 05, 2019 | 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). - |
Malaria, cerebral, susceptibility to Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Sep 01, 2013 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.
MutationTaster
Benign
P;P
PrimateAI
Benign
T
PROVEAN
Benign
N;.
REVEL
Benign
Sift
Benign
T;.
Sift4G
Benign
T;T
Polyphen
B;.
Vest4
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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Calibrated prediction
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at