NM_000201.3:c.*373C>T

Variant names:

• chr19-10285660-C-T
• rs3093032
• NM_000201.3:c.*373C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 frequency of 0.102 in 209,964 control chromosomes in the GnomAD database, including 1,402 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 0.097 (954 hom., cov: 32)
  • Exomes 𝑓: 0.11 (448 hom.)
• Consequence: ICAM1 NM_000201.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.243
• Publications: 48 publications found

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]

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

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.138 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ICAM1	NM_000201.3	c.*373C>T		3_prime_UTR_variant	Exon 7 of 7	ENST00000264832.8	NP_000192.2
ICAM4-AS1	NR_186335.1	n.*141G>A		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ICAM1	ENST00000264832.8	c.*373C>T		3_prime_UTR_variant	Exon 7 of 7	1	NM_000201.3	ENSP00000264832.2

Frequencies

GnomAD3 genomes AF: 0.0973 AC: 14805 AN: 152092 Hom.: 955 Cov.: 32

Gnomad AFR AF: 0.0246

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.0744

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.0468

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.104

GnomAD4 exome AF: 0.114 AC: 6571 AN: 57754 Hom.: 448 Cov.: 0 AF XY: 0.114 AC XY: 3455 AN XY: 30182

African (AFR) AF: 0.0237 AC: 53 AN: 2238

American (AMR) AF: 0.0743 AC: 289 AN: 3890

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 200 AN: 1692

East Asian (EAS) AF: 0.0333 AC: 109 AN: 3276

South Asian (SAS) AF: 0.108 AC: 675 AN: 6226

European-Finnish (FIN) AF: 0.118 AC: 233 AN: 1976

Middle Eastern (MID) AF: 0.194 AC: 48 AN: 248

European-Non Finnish (NFE) AF: 0.132 AC: 4595 AN: 34940

Other (OTH) AF: 0.113 AC: 369 AN: 3268

GnomAD4 genome AF: 0.0972 AC: 14802 AN: 152210 Hom.: 954 Cov.: 32 AF XY: 0.0968 AC XY: 7205 AN XY: 74426

African (AFR) AF: 0.0245 AC: 1019 AN: 41542

American (AMR) AF: 0.0742 AC: 1134 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 448 AN: 3472

East Asian (EAS) AF: 0.0469 AC: 243 AN: 5182

South Asian (SAS) AF: 0.106 AC: 510 AN: 4832

European-Finnish (FIN) AF: 0.146 AC: 1549 AN: 10594

Middle Eastern (MID) AF: 0.182 AC: 53 AN: 292

European-Non Finnish (NFE) AF: 0.141 AC: 9554 AN: 67986

Other (OTH) AF: 0.108 AC: 229 AN: 2114

Alfa AF: 0.122 Hom.: 2613

Bravo AF: 0.0884

Asia WGS AF: 0.0910 AC: 317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.9
DANN	Benign	0.52
PhyloP100		-0.24
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3093032; hg19: chr19-10396336;