chr19-10274741-C-T

Variant names:

• chr19-10274741-C-T
• rs5030351
• NM_000201.3:c.68-24C>T

Variant summary

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

The NM_000201.3(ICAM1):​c.68-24C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0119 in 1,605,550 control chromosomes in the GnomAD database, including 1,922 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 0.062 (989 hom., cov: 31)
  • Exomes 𝑓: 0.0066 (933 hom.)
• Consequence: ICAM1 NM_000201.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0970
• Publications: 7 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.211 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ICAM1	NM_000201.3	MANE Select	c.68-24C>T		intron	N/A	NP_000192.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ICAM1	ENST00000264832.8	TSL:1 MANE Select	c.68-24C>T		intron	N/A	ENSP00000264832.2
	ICAM1	ENST00000423829.2	TSL:2	c.67+3515C>T		intron	N/A	ENSP00000413124.2
	ICAM1	ENST00000588645.1	TSL:2	c.68-24C>T		intron	N/A	ENSP00000465680.1

Frequencies

GnomAD3 genomes AF: 0.0620 AC: 9440 AN: 152140 Hom.: 986 Cov.: 31

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0251

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000827

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.000588

Gnomad OTH AF: 0.0497

GnomAD2 exomes AF: 0.0165 AC: 4099 AN: 247692 AF XY: 0.0119

Gnomad AFR exome AF: 0.223

Gnomad AMR exome AF: 0.0111

Gnomad ASJ exome AF: 0.000103

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000607

Gnomad OTH exome AF: 0.00677

GnomAD4 exome AF: 0.00660 AC: 9593 AN: 1453292 Hom.: 933 Cov.: 31 AF XY: 0.00564 AC XY: 4070 AN XY: 721542

African (AFR) AF: 0.228 AC: 7581 AN: 33240

American (AMR) AF: 0.0126 AC: 558 AN: 44390

Ashkenazi Jewish (ASJ) AF: 0.0000775 AC: 2 AN: 25806

East Asian (EAS) AF: 0.00 AC: 0 AN: 39484

South Asian (SAS) AF: 0.000536 AC: 46 AN: 85886

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 52378

Middle Eastern (MID) AF: 0.0112 AC: 64 AN: 5722

European-Non Finnish (NFE) AF: 0.000369 AC: 408 AN: 1106368

Other (OTH) AF: 0.0156 AC: 934 AN: 60018

GnomAD4 genome AF: 0.0621 AC: 9460 AN: 152258 Hom.: 989 Cov.: 31 AF XY: 0.0603 AC XY: 4491 AN XY: 74454

African (AFR) AF: 0.215 AC: 8928 AN: 41530

American (AMR) AF: 0.0250 AC: 383 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5182

South Asian (SAS) AF: 0.000621 AC: 3 AN: 4832

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10614

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.000588 AC: 40 AN: 68010

Other (OTH) AF: 0.0491 AC: 104 AN: 2116

Alfa AF: 0.0237 Hom.: 421

Bravo AF: 0.0713

Asia WGS AF: 0.0120 AC: 41 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	9.1
DANN	Benign	0.70
PhyloP100		0.097
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: rs5030351; hg19: chr19-10385417;