rs5030390

chr19-10271861-G-A

Variant summary

Our verdict is Benign. Variant got -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

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 -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ICAM1	NM_000201.3	c.67+635G>A		intron_variant		ENST00000264832.8
LIMASI	XR_007067138.1	n.131-5067C>T		intron_variant, non_coding_transcript_variant
LIMASI	XR_007067137.1	n.131-5067C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ICAM1	ENST00000264832.8	c.67+635G>A		intron_variant		1	NM_000201.3	P1
LIMASI	ENST00000592893.1	n.142-11433C>T		intron_variant, non_coding_transcript_variant		3
ICAM1	ENST00000423829.2	c.67+635G>A		intron_variant		2
ICAM1	ENST00000588645.1	c.67+635G>A		intron_variant		2

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

Gnomad4 AFR AF: 0.0146

Gnomad4 AMR AF: 0.0543

Gnomad4 ASJ AF: 0.0820

Gnomad4 EAS AF: 0.00213

Gnomad4 SAS AF: 0.0278

Gnomad4 FIN AF: 0.0449

Gnomad4 NFE AF: 0.0771

Gnomad4 OTH AF: 0.0604

Alfa AF: 0.0710 Hom.: 231

Bravo AF: 0.0522

Asia WGS AF: 0.0150 AC: 53 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	2.5
Dann	Benign	0.39

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: rs5030390; hg19: chr19-10382537;