rs5030341

chr19-10272596-ACT-A

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_000201.3(ICAM1):c.67+1373_67+1374del variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.36 (7750 hom., cov: 0)
• Consequence: ICAM1 NM_000201.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780

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)

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ICAM1	NM_000201.3	c.67+1373_67+1374del		intron_variant		ENST00000264832.8
LIMASI	XR_007067138.1	n.131-5804_131-5803del		intron_variant, non_coding_transcript_variant
LIMASI	XR_007067137.1	n.131-5804_131-5803del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ICAM1	ENST00000264832.8	c.67+1373_67+1374del		intron_variant		1	NM_000201.3	P1
LIMASI	ENST00000592893.1	n.142-12170_142-12169del		intron_variant, non_coding_transcript_variant		3
ICAM1	ENST00000423829.2	c.67+1373_67+1374del		intron_variant		2
ICAM1	ENST00000588645.1	c.67+1373_67+1374del		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.358 AC: 44027 AN: 123130 Hom.: 7746 Cov.: 0

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.0934

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.482

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.363

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.358 AC: 44042 AN: 123164 Hom.: 7750 Cov.: 0 AF XY: 0.357 AC XY: 20581 AN XY: 57626

Gnomad4 AFR AF: 0.317

Gnomad4 AMR AF: 0.327

Gnomad4 ASJ AF: 0.355

Gnomad4 EAS AF: 0.0936

Gnomad4 SAS AF: 0.254

Gnomad4 FIN AF: 0.426

Gnomad4 NFE AF: 0.399

Gnomad4 OTH AF: 0.363

Alfa AF: 0.254 Hom.: 14

Asia WGS AF: 0.168 AC: 569 AN: 3386

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs5030341; hg19: chr19-10383272;