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GeneBe

rs5498

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_000201.3(ICAM1):c.1405A>G(p.Lys469Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 151900 control chromosomes in the gnomAD Genomes database, including 11683 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.37 ( 11683 hom., cov: 32)
Exomes 𝑓: 0.44 ( 25472 hom. )

Consequence

ICAM1
NM_000201.3 missense

Scores

18

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.186

Links

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
?
Computational evidence support a benign effect (MetaRNN=1.9145012E-4).
BP6
?
Variant 19-10285007-A-G is Benign according to our data. Variant chr19-10285007-A-G is described in Lovd as [Benign].
BA1
?
GnomAd highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ICAM1NM_000201.3 linkuse as main transcriptc.1405A>G p.Lys469Glu missense_variant 6/7 ENST00000264832.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ICAM1ENST00000264832.8 linkuse as main transcriptc.1405A>G p.Lys469Glu missense_variant 6/71 NM_000201.3 P1
LIMASIENST00000592893.1 linkuse as main transcriptn.102T>C non_coding_transcript_exon_variant 1/33
ICAM1ENST00000423829.2 linkuse as main transcriptc.739A>G p.Lys247Glu missense_variant 4/52

Frequencies

GnomAD3 genomes
AF:
0.372
AC:
56534
AN:
151900
Hom.:
11683
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.185
Gnomad AMI
AF:
0.566
Gnomad AMR
AF:
0.501
Gnomad ASJ
AF:
0.473
Gnomad EAS
AF:
0.288
Gnomad SAS
AF:
0.479
Gnomad FIN
AF:
0.460
Gnomad MID
AF:
0.383
Gnomad NFE
AF:
0.433
Gnomad OTH
AF:
0.420
GnomAD3 exomes
AF:
0.438
AC:
109733
AN:
250628
Hom.:
25472
AF XY:
0.442
AC XY:
59930
AN XY:
135520
show subpopulations
Gnomad AFR exome
AF:
0.176
Gnomad AMR exome
AF:
0.600
Gnomad ASJ exome
AF:
0.466
Gnomad EAS exome
AF:
0.275
Gnomad SAS exome
AF:
0.488
Gnomad FIN exome
AF:
0.457
Gnomad NFE exome
AF:
0.432
Gnomad OTH exome
AF:
0.447
GnomAD4 exome
AF:
0.429
AC:
626242
AN:
1461044
Hom.:
136824
AF XY:
0.431
AC XY:
313016
AN XY:
726776
show subpopulations
Gnomad4 AFR exome
AF:
0.173
Gnomad4 AMR exome
AF:
0.586
Gnomad4 ASJ exome
AF:
0.462
Gnomad4 EAS exome
AF:
0.342
Gnomad4 SAS exome
AF:
0.487
Gnomad4 FIN exome
AF:
0.454
Gnomad4 NFE exome
AF:
0.427
Gnomad4 OTH exome
AF:
0.421
Alfa
AF:
0.425
Hom.:
35039
Bravo
AF:
0.369
TwinsUK
AF:
0.412
AC:
1526
ALSPAC
AF:
0.422
AC:
1628
ESP6500AA
AF:
0.193
AC:
849
ESP6500EA
AF:
0.431
AC:
3708
ExAC
AF:
0.428
AC:
51923
Asia WGS
AF:
0.402
AC:
1400
AN:
3478
EpiCase
AF:
0.439
EpiControl
AF:
0.442

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.055
BayesDel_addAF
Benign
-0.85
T
BayesDel_noAF
Benign
-0.85
Cadd
Benign
5.4
Dann
Benign
0.32
DEOGEN2
Benign
0.016
T;.
Eigen
Benign
-1.6
Eigen_PC
Benign
-1.6
FATHMM_MKL
Benign
0.0067
N
LIST_S2
Benign
0.042
T;T
MetaRNN
Benign
0.00019
T;T
MetaSVM
Benign
-0.92
T
MutationAssessor
Benign
-1.5
N;.
MutationTaster
Benign
1.0
P;P
PrimateAI
Benign
0.30
T
PROVEAN
Benign
1.4
N;N
REVEL
Benign
0.020
Sift
Benign
1.0
T;T
Sift4G
Benign
1.0
T;T
Polyphen
0.0
B;B
Vest4
0.018
MPC
0.22
ClinPred
0.00058
T
GERP RS
-2.6
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.037
gMVP
0.31

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.070
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs5498; hg19: chr19-10395683; COSMIC: COSV53424462; COSMIC: COSV53424462;