NM_000201.3:c.*373C>T

Variant names:

Variant summary

Our verdict is The variant received -12 classification points (ACMG Germline Pathogenicity v2019). BA1BP4_Strong

The NM_000201.3(ICAM1):c.*373C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a cumulative frequency of 0.102 (AC=21,373) in the gnomAD database across 209,964 control chromosomes, including 1,402 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.15. In-silico predictor (BayesDel (noAF)) classifies this variant as likely benign. Splicing prediction tools (SpliceAI) predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.097 ( 954 hom., cov: 32)

Exomes 𝑓: 0.11 ( 448 hom. )

Consequence

ICAM1
NM_000201.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.243

Publications

48 publications found

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:

ICAM4-AS1 (HGNC:55990): (ICAM4 antisense RNA 1)

ICAM4-AS1 links:

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new If you want to explore the variant's impact on the transcript NM_000201.3, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

Classification according to ACMG Germline Pathogenicity v2019

Classification was made for transcript

Our verdict: Benign. The variant received -12 points.

BP4

Computational evidence supports benign — no pathogenic computational or splicing signal (BP4); Splicing verdict: benign (Strong).; Germline computational verdict: benign (Strong).

BA1

GnomAD effective popmax AF >5% — BA1 stand-alone benign; GnomAD reliable popmax AF = 0.1500 — exceeds 5%% threshold (BA1 applied)

Variant Effect in Transcripts

Automated classification analysis was done for transcript: NM_000201.3. You can select a different transcript below to see updated classification assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ICAM1	NM_000201.3	MANE Select	c.*373C>T		3_prime_UTR	Exon 7 of 7	NP_000192.2	P05362
	ICAM4-AS1	NR_186335.1		n.*141G>A		downstream_gene	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ICAM1	ENST00000264832.8	TSL:1 MANE Select	c.*373C>T	3_prime_UTR	Exon 7 of 7	ENSP00000264832.2	P05362
ICAM1	ENST00000902798.1		c.*373C>T	3_prime_UTR	Exon 6 of 6	ENSP00000572857.1	A0ACI8SAS2
ICAM1	ENST00000935832.1		c.*373C>T	3_prime_UTR	Exon 6 of 6	ENSP00000605891.1	A0ACI8TWK6

Frequencies

Allele frequencies (AF), counts (AC/AN), homozygotes and coverage

Common (AF > 0.05 / Hom > 5)

Rare (AF ≤ 0.0001 / Hom ≤ 1)

Source / population	AF	AC	Hom	AN	Coverage
Global population databases 5 sources Large-scale international reference populations
GnomAD3 genomes	0.0973	14805	955	152092	32
GnomAD4 exome	0.114	6571	448	57754	0
GnomAD4 genome	0.0972	14802	954	152210	32
TOPMed (Bravo)	0.0884	23411	1425	264690
ALFA (dbGaP/dbSNP Allele Frequency Aggregator)	0.121	41190	2852	339220
Local & regional cohorts 10 sources Population-specific and national genomic databases
ABraOM SABE-WGS-1171	0.109	255	20	2342
ChinaMAP Phase 1	0.0489
Denmark Genome	0.137	41		300
GenomeAsia100K	0.0910	317		3478
Korea4K (4,157 Koreans)	0.0410	297		7234
Qatari Genome	0.204	36		176
ToMMo 61KJPN (+60KJPN MNV)	0.0199	2441	26	122510
Turkish Variome	0.179	276	22	1544
UK10K	0.143	1082		7562
WBBC (Westlake BioBank for Chinese) pilot	0.0532	477	15	8960

Showing 15 sources

Case/control cohorts

Cohort	Cases			Controls
Cohort	AF	AC	AN	AF	AC	AN
SCHEMA (Schizophrenia)	0.0341	874	25648	0.0258	905	35100

Showing 1 cohortAllele count / allele number. AF is computed from the counts for ASC (not provided by the source).

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated prediction	Prediction	Score
AlphaGenome AVI	Benign	-	3.8
BayesDel_noAF	Benign	-	-0.81
CADD	Benign	-	1.9
DANN	Benign	-	0.52
GPN-Star LLR	N/A	-	-0.59
GPN-Star score	N/A	-	0.59
Mutation Taster	N/A	polymorphism (auto)	100/0
PhyloP100	Benign	-	-0.24
RBP_binding_hub_radar	N/A	-	0.0
RBP_regulation_power_radar	N/A	-	1.1

Showing 10 of 10 scores

Splicing Scores

Algorithm	Calibrated prediction	Prediction	Score
Pangolin (max)	Benign	-	0.0
SpliceAI score (max)	Benign	- Details are displayed if max score is > 0.2	0.0

Showing 2 of 2 scores

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

Classification according to ACMG Germline Pathogenicity v2019

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Case/control cohorts

ClinVar

Computational Scores

Splicing Scores

Publications

Other links and lift over