Genetic Variant ICAM1:c.-9A>C (chr19-10271151-A-C) – ACMG Classification: Benign (-13 pts)

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

Genomes: 𝑓 0.063 ( 997 hom., cov: 32)

Exomes 𝑓: 0.0065 ( 908 hom. )

Consequence

ICAM1
NM_000201.3 5_prime_UTR

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.610

Variant links:

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]

ICAM1 links:

LIMASI (HGNC:56357): (lncRNA inflammatory and mucous response associated, antisense to ICAM1)

LIMASI links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.02).

BP6

Variant 19-10271151-A-C is Benign according to our data. Variant chr19-10271151-A-C is described in ClinVar as [Benign]. Clinvar id is 3056696.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
ICAM1	NM_000201.3 link	c.-9A>C	5_prime_UTR_variant	Exon 1 of 7	ENST00000264832.8	NP_000192.2	P05362A0A384MEK5
LIMASI	XR_007067137.1 link	n.131-4357T>G	intron_variant	Intron 1 of 3
LIMASI	XR_007067138.1 link	n.131-4357T>G	intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ICAM1	ENST00000264832 link	c.-9A>C	5_prime_UTR_variant	Exon 1 of 7	1	NM_000201.3	ENSP00000264832.2	P05362
ICAM1	ENST00000423829 link	c.-9A>C	5_prime_UTR_variant	Exon 1 of 5	2		ENSP00000413124.2	E7ESS4
ICAM1	ENST00000588645 link	c.-9A>C	5_prime_UTR_variant	Exon 1 of 4	2		ENSP00000465680.1	K7EKL8
LIMASI	ENST00000592893.1 link	n.142-10723T>G	intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes

AF:

0.0629

AC:

9572

AN:

152100

Hom.:

995

Cov.:

show subpopulations

Gnomad AFR

AF:

0.218

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0257

Gnomad ASJ

AF:

0.00173

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000828

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00318

Gnomad NFE

AF:

0.000632

Gnomad OTH

AF:

0.0531

GnomAD3 exomes

AF:

0.0159

AC:

3922

AN:

246402

Hom.:

372

AF XY:

0.0116

AC XY:

1551

AN XY:

134016

show subpopulations

Gnomad AFR exome

AF:

0.222

Gnomad AMR exome

AF:

0.00997

Gnomad ASJ exome

AF:

0.00182

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000494

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000667

Gnomad OTH exome

AF:

0.00619

GnomAD4 exome

AF:

0.00647

AC:

9447

AN:

1459952

Hom.:

908

Cov.:

AF XY:

0.00547

AC XY:

3973

AN XY:

726274

show subpopulations

Gnomad4 AFR exome

AF:

0.223

Gnomad4 AMR exome

AF:

0.0115

Gnomad4 ASJ exome

AF:

0.00127

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000523

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000392

Gnomad4 OTH exome

AF:

0.0149

GnomAD4 genome

AF:

0.0629

AC:

9582

AN:

152218

Hom.:

997

Cov.:

AF XY:

0.0610

AC XY:

4544

AN XY:

74434

show subpopulations

Gnomad4 AFR

AF:

0.217

Gnomad4 AMR

AF:

0.0256

Gnomad4 ASJ

AF:

0.00173

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000621

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000632

Gnomad4 OTH

AF:

0.0525

Alfa

AF:

0.0330

Hom.:

286

Bravo

AF:

0.0724

Asia WGS

AF:

0.0100

AC:

AN:

3478

EpiCase

AF:

0.000654

EpiControl

AF:

0.000831

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

ICAM1-related disorder

Benign:1

Dec 05, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

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: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

2.0

DANN

Benign

0.40

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over