rs5030390

Variant names:

• chr19-10271861-G-A
• rs5030390
• NM_000201.3:c.67+635G>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.67+635G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0509 in 152,022 control chromosomes in the GnomAD database, including 261 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 0.051 (261 hom., cov: 32)
• Consequence: ICAM1 NM_000201.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.423
• Publications: 27 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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0753 is higher than 0.05.

Variant Effect in Transcripts

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

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ICAM1	NM_000201.3	MANE Select	c.67+635G>A		intron	N/A	NP_000192.2	A0A384MEK5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ICAM1	ENST00000264832.8	TSL:1 MANE Select	c.67+635G>A		intron	N/A	ENSP00000264832.2	P05362
	ICAM1	ENST00000902798.1		c.67+635G>A		intron	N/A	ENSP00000572857.1
	ICAM1	ENST00000935832.1		c.67+635G>A		intron	N/A	ENSP00000605891.1

Frequencies

GnomAD3 genomes AF: 0.0510 AC: 7745 AN: 151904 Hom.: 261 Cov.: 32

Gnomad AFR AF: 0.0147

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0543

Gnomad ASJ AF: 0.0820

Gnomad EAS AF: 0.00213

Gnomad SAS AF: 0.0284

Gnomad FIN AF: 0.0449

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0771

Gnomad OTH AF: 0.0600

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

GnomAD4 genome AF: 0.0509 AC: 7739 AN: 152022 Hom.: 261 Cov.: 32 AF XY: 0.0490 AC XY: 3642 AN XY: 74282

African (AFR) AF: 0.0146 AC: 606 AN: 41484

American (AMR) AF: 0.0543 AC: 826 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.0820 AC: 284 AN: 3462

East Asian (EAS) AF: 0.00213 AC: 11 AN: 5164

South Asian (SAS) AF: 0.0278 AC: 134 AN: 4816

European-Finnish (FIN) AF: 0.0449 AC: 476 AN: 10594

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0771 AC: 5239 AN: 67970

Other (OTH) AF: 0.0604 AC: 127 AN: 2104

Alfa AF: 0.0686 Hom.: 372

Bravo AF: 0.0522

Asia WGS AF: 0.0150 AC: 53 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.5
DANN	Benign	0.39
PhyloP100		-0.42
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: rs5030390; hg19: chr19-10382537;