NM_003259.4:c.82+297G>A

Variant names:

• chr19-10290422-G-A
• rs2075741
• NM_003259.4:c.82+297G>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_003259.4(ICAM5):​c.82+297G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ICAM5 NM_003259.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.784
• Publications: 16 publications found

Genes affected

ICAM5 (HGNC:5348): (intercellular adhesion molecule 5) The protein encoded by this gene is a member of the intercellular adhesion molecule (ICAM) family. All ICAM proteins are type I transmembrane glycoproteins, contain 2-9 immunoglobulin-like C2-type domains, and bind to the leukocyte adhesion LFA-1 protein. This protein is expressed on the surface of telencephalic neurons and displays two types of adhesion activity, homophilic binding between neurons and heterophilic binding between neurons and leukocytes. It may be a critical component in neuron-microglial cell interactions in the course of normal development or as part of neurodegenerative diseases. [provided by RefSeq, Jul 2008]

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

ENSG00000294616 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ICAM5	NM_003259.4	c.82+297G>A		intron_variant	Intron 1 of 10	ENST00000221980.5	NP_003250.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ICAM5	ENST00000221980.5	c.82+297G>A		intron_variant	Intron 1 of 10	1	NM_003259.4	ENSP00000221980.3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 217242 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 111770

African (AFR) AF: 0.00 AC: 0 AN: 5854

American (AMR) AF: 0.00 AC: 0 AN: 7812

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 7816

East Asian (EAS) AF: 0.00 AC: 0 AN: 16554

South Asian (SAS) AF: 0.00 AC: 0 AN: 13348

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 15328

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1110

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 135390

Other (OTH) AF: 0.00 AC: 0 AN: 14030

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 671

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	9.8
DANN	Benign	0.77
PhyloP100		-0.78
PromoterAI		0.0014	Neutral
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

Other links and lift over

dbSNP: rs2075741; hg19: chr19-10401098;