rs5030347

Variant names:

• chr19-10273928-C-A
• rs5030347
• NM_000201.3:c.68-837C>A

Variant summary

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

The NM_000201.3(ICAM1):​c.68-837C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 151,846 control chromosomes in the GnomAD database, including 1,849 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 0.14 (1849 hom., cov: 31)
• Consequence: ICAM1 NM_000201.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.193
• Publications: 4 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)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ICAM1	NM_000201.3	c.68-837C>A		intron_variant	Intron 1 of 6	ENST00000264832.8	NP_000192.2
LIMASI	XR_007067137.1	n.131-7134G>T		intron_variant	Intron 1 of 3
LIMASI	XR_007067138.1	n.131-7134G>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ICAM1	ENST00000264832.8	c.68-837C>A		intron_variant	Intron 1 of 6	1	NM_000201.3	ENSP00000264832.2

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20560 AN: 151728 Hom.: 1848 Cov.: 31

Gnomad AFR AF: 0.0344

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.0755

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.135 AC: 20563 AN: 151846 Hom.: 1849 Cov.: 31 AF XY: 0.132 AC XY: 9775 AN XY: 74172

African (AFR) AF: 0.0343 AC: 1419 AN: 41430

American (AMR) AF: 0.100 AC: 1526 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 613 AN: 3464

East Asian (EAS) AF: 0.00213 AC: 11 AN: 5176

South Asian (SAS) AF: 0.0763 AC: 368 AN: 4820

European-Finnish (FIN) AF: 0.192 AC: 2020 AN: 10494

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.207 AC: 14044 AN: 67936

Other (OTH) AF: 0.122 AC: 257 AN: 2104

Alfa AF: 0.180 Hom.: 354

Bravo AF: 0.123

Asia WGS AF: 0.0300 AC: 105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.69
DANN	Benign	0.43
PhyloP100		0.19
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: rs5030347; hg19: chr19-10384604;