rs3181092

Variant names:

• chr1-100739088-A-G
• rs3181092
• ENST00000762830.1:n.85-3335T>C

Variant summary

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

The ENST00000762830.1(ENSG00000299357):​n.85-3335T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.53 in 152,072 control chromosomes in the GnomAD database, including 23,535 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 0.53 (23535 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000299357 ENST00000762830.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91
• Publications: 15 publications found

Genes affected

ENSG00000299357 (HGNC:):

VCAM1 (HGNC:12663): (vascular cell adhesion molecule 1) This gene is a member of the Ig superfamily and encodes a cell surface sialoglycoprotein expressed by cytokine-activated endothelium. This type I membrane protein mediates leukocyte-endothelial cell adhesion and signal transduction, and may play a role in the development of artherosclerosis and rheumatoid arthritis. Three alternatively spliced transcripts encoding different isoforms have been described for this gene. [provided by RefSeq, Dec 2010]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000762830.1. 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
	VCAM1	NM_001078.4	MANE Select	c.*805A>G		downstream_gene	N/A	NP_001069.1
	VCAM1	NM_001199834.2		c.*805A>G		downstream_gene	N/A	NP_001186763.1
	VCAM1	NM_080682.3		c.*805A>G		downstream_gene	N/A	NP_542413.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299357	ENST00000762830.1		n.85-3335T>C		intron	N/A
	VCAM1	ENST00000294728.7	TSL:1 MANE Select	c.*805A>G		downstream_gene	N/A	ENSP00000294728.2
	VCAM1	ENST00000347652.6	TSL:1	c.*805A>G		downstream_gene	N/A	ENSP00000304611.2

Frequencies

GnomAD3 genomes AF: 0.530 AC: 80568 AN: 151954 Hom.: 23525 Cov.: 33

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.519

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.530 AC: 80603 AN: 152072 Hom.: 23535 Cov.: 33 AF XY: 0.528 AC XY: 39220 AN XY: 74336

African (AFR) AF: 0.286 AC: 11875 AN: 41496

American (AMR) AF: 0.512 AC: 7811 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1763 AN: 3470

East Asian (EAS) AF: 0.495 AC: 2559 AN: 5172

South Asian (SAS) AF: 0.538 AC: 2594 AN: 4824

European-Finnish (FIN) AF: 0.682 AC: 7192 AN: 10548

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.661 AC: 44920 AN: 67982

Other (OTH) AF: 0.524 AC: 1106 AN: 2112

Alfa AF: 0.578 Hom.: 14000

Bravo AF: 0.506

Asia WGS AF: 0.532 AC: 1850 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.031
DANN	Benign	0.61
PhyloP100		-1.9
Mutation Taster		=100/0	polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3181092; hg19: chr1-101204644;