chr19-10271605-C-T

Position:

• chr19-10271605-C-T

Variant summary

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

The ENST00000264832.8(ICAM1):​c.67+379C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0483 in 152,174 control chromosomes in the GnomAD database, including 189 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 0.048 (189 hom., cov: 32)
• Consequence: ICAM1 ENST00000264832.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.331

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=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ICAM1	NM_000201.3	c.67+379C>T		intron_variant		ENST00000264832.8	NP_000192.2
LIMASI	XR_007067138.1	n.131-4811G>A		intron_variant, non_coding_transcript_variant
LIMASI	XR_007067137.1	n.131-4811G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ICAM1	ENST00000264832.8	c.67+379C>T		intron_variant		1	NM_000201.3	ENSP00000264832	P1
LIMASI	ENST00000592893.1	n.142-11177G>A		intron_variant, non_coding_transcript_variant		3
ICAM1	ENST00000423829.2	c.67+379C>T		intron_variant		2		ENSP00000413124
ICAM1	ENST00000588645.1	c.67+379C>T		intron_variant		2		ENSP00000465680

Frequencies

GnomAD3 genomes AF: 0.0483 AC: 7342 AN: 152056 Hom.: 189 Cov.: 32

Gnomad AFR AF: 0.0450

Gnomad AMI AF: 0.0582

Gnomad AMR AF: 0.0392

Gnomad ASJ AF: 0.0516

Gnomad EAS AF: 0.0353

Gnomad SAS AF: 0.0721

Gnomad FIN AF: 0.0318

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0536

Gnomad OTH AF: 0.0505

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

GnomAD4 genome AF: 0.0483 AC: 7349 AN: 152174 Hom.: 189 Cov.: 32 AF XY: 0.0472 AC XY: 3511 AN XY: 74398

Gnomad4 AFR AF: 0.0450

Gnomad4 AMR AF: 0.0390

Gnomad4 ASJ AF: 0.0516

Gnomad4 EAS AF: 0.0354

Gnomad4 SAS AF: 0.0728

Gnomad4 FIN AF: 0.0318

Gnomad4 NFE AF: 0.0536

Gnomad4 OTH AF: 0.0509

Alfa AF: 0.0466 Hom.: 17

Bravo AF: 0.0472

Asia WGS AF: 0.0550 AC: 191 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.7
DANN	Benign	0.93

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: rs5030340; hg19: chr19-10382281;