19-10275067-C-T

Variant names:

• chr19-10275067-C-T
• rs5030352
• NM_000201.3:c.331+39C>T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_000201.3(ICAM1):​c.331+39C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00672 in 1,600,218 control chromosomes in the GnomAD database, including 47 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 0.0051 (4 hom., cov: 33)
  • Exomes 𝑓: 0.0069 (43 hom.)
• Consequence: ICAM1 NM_000201.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.372

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.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BS2: High Homozygotes in GnomAd4 at 4 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ICAM1	NM_000201.3	c.331+39C>T		intron_variant	Intron 2 of 6	ENST00000264832.8	NP_000192.2
LIMASI	XR_007067137.1	n.130+8254G>A		intron_variant	Intron 1 of 3
LIMASI	XR_007067138.1	n.130+8254G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ICAM1	ENST00000264832.8	c.331+39C>T		intron_variant	Intron 2 of 6	1	NM_000201.3	ENSP00000264832.2
ICAM1	ENST00000423829.2	c.67+3841C>T		intron_variant	Intron 1 of 4	2		ENSP00000413124.2
ICAM1	ENST00000588645.1	c.331+39C>T		intron_variant	Intron 2 of 3	2		ENSP00000465680.1
LIMASI	ENST00000592893.1	n.141+9901G>A		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.00514 AC: 782 AN: 152146 Hom.: 4 Cov.: 33

Gnomad AFR AF: 0.00147

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000917

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00124

Gnomad FIN AF: 0.0117

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00834

Gnomad OTH AF: 0.00430

GnomAD3 exomes AF: 0.00544 AC: 1303 AN: 239548 Hom.: 5 AF XY: 0.00565 AC XY: 739 AN XY: 130872

Gnomad AFR exome AF: 0.00112

Gnomad AMR exome AF: 0.00109

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.000220

Gnomad SAS exome AF: 0.000792

Gnomad FIN exome AF: 0.0108

Gnomad NFE exome AF: 0.00924

Gnomad OTH exome AF: 0.00422

GnomAD4 exome AF: 0.00689 AC: 9976 AN: 1447954 Hom.: 43 Cov.: 32 AF XY: 0.00675 AC XY: 4852 AN XY: 719246

Gnomad4 AFR exome AF: 0.00109

Gnomad4 AMR exome AF: 0.00136

Gnomad4 ASJ exome AF: 0.000193

Gnomad4 EAS exome AF: 0.000177

Gnomad4 SAS exome AF: 0.000936

Gnomad4 FIN exome AF: 0.0103

Gnomad4 NFE exome AF: 0.00814

Gnomad4 OTH exome AF: 0.00478

GnomAD4 genome AF: 0.00514 AC: 783 AN: 152264 Hom.: 4 Cov.: 33 AF XY: 0.00517 AC XY: 385 AN XY: 74444

Gnomad4 AFR AF: 0.00147

Gnomad4 AMR AF: 0.000916

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00145

Gnomad4 FIN AF: 0.0117

Gnomad4 NFE AF: 0.00834

Gnomad4 OTH AF: 0.00425

Alfa AF: 0.00487 Hom.: 1423

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.4
DANN	Benign	0.97
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs5030352; hg19: chr19-10385743;