19-10286547-C-T

Variant names:

• chr19-10286547-C-T
• rs923366
• NM_000201.3:c.*1260C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000201.3(ICAM1):​c.*1260C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.355 in 153,606 control chromosomes in the GnomAD database, including 11,277 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 0.36 (11102 hom., cov: 30)
  • Exomes 𝑓: 0.31 (175 hom.)
• Consequence: ICAM1 NM_000201.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.06

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]

ICAM4-AS1 (HGNC:55990): (ICAM4 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ICAM1	NM_000201.3	c.*1260C>T		3_prime_UTR_variant	Exon 7 of 7	ENST00000264832.8	NP_000192.2
ICAM4-AS1	NR_186335.1	n.2473G>A		non_coding_transcript_exon_variant	Exon 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ICAM1	ENST00000264832.8	c.*1260C>T		3_prime_UTR_variant	Exon 7 of 7	1	NM_000201.3	ENSP00000264832.2
ICAM4-AS1	ENST00000589379.1	n.2473G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.357 AC: 53107 AN: 148938 Hom.: 11108 Cov.: 30

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.372

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.418

GnomAD4 exome AF: 0.307 AC: 1402 AN: 4568 Hom.: 175 Cov.: 0 AF XY: 0.310 AC XY: 709 AN XY: 2290

Gnomad4 AFR exome AF: 0.0773

Gnomad4 AMR exome AF: 0.366

Gnomad4 ASJ exome AF: 0.400

Gnomad4 EAS exome AF: 0.244

Gnomad4 SAS exome AF: 0.472

Gnomad4 FIN exome AF: 0.348

Gnomad4 NFE exome AF: 0.320

Gnomad4 OTH exome AF: 0.274

GnomAD4 genome AF: 0.356 AC: 53091 AN: 149038 Hom.: 11102 Cov.: 30 AF XY: 0.362 AC XY: 26295 AN XY: 72634

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.495

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.331

Gnomad4 SAS AF: 0.512

Gnomad4 FIN AF: 0.467

Gnomad4 NFE AF: 0.435

Gnomad4 OTH AF: 0.418

Alfa AF: 0.422 Hom.: 13355

Bravo AF: 0.349

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.17
DANN	Benign	0.45
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs923366; hg19: chr19-10397223;