rs3917010

Variant names:

• chr1-100725310-A-C
• rs3917010
• NM_001078.4:c.928+420A>C

Your query was ambiguous. Multiple possible variants found:

• chr1-100725310-A-C
• chr1-100725310-A-G

Variant summary

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

The NM_001078.4(VCAM1):​c.928+420A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 151,680 control chromosomes in the GnomAD database, including 3,189 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 0.18 (3189 hom., cov: 31)
• Consequence: VCAM1 NM_001078.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.92
• Publications: 12 publications found

Genes affected

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]

ENSG00000299357 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001078.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VCAM1	NM_001078.4	MANE Select	c.928+420A>C		intron	N/A	NP_001069.1	P19320-1
	VCAM1	NM_001199834.2		c.742+420A>C		intron	N/A	NP_001186763.1	P19320-3
	VCAM1	NM_080682.3		c.928+420A>C		intron	N/A	NP_542413.1	P19320-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VCAM1	ENST00000294728.7	TSL:1 MANE Select	c.928+420A>C		intron	N/A	ENSP00000294728.2	P19320-1
	VCAM1	ENST00000347652.6	TSL:1	c.928+420A>C		intron	N/A	ENSP00000304611.2	P19320-2
	VCAM1	ENST00000855907.1		c.928+420A>C		intron	N/A	ENSP00000525966.1

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27809 AN: 151562 Hom.: 3188 Cov.: 31

Gnomad AFR AF: 0.0473

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.183 AC: 27809 AN: 151680 Hom.: 3189 Cov.: 31 AF XY: 0.188 AC XY: 13948 AN XY: 74086

African (AFR) AF: 0.0472 AC: 1956 AN: 41446

American (AMR) AF: 0.240 AC: 3642 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 602 AN: 3466

East Asian (EAS) AF: 0.258 AC: 1321 AN: 5118

South Asian (SAS) AF: 0.386 AC: 1854 AN: 4802

European-Finnish (FIN) AF: 0.216 AC: 2276 AN: 10520

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.229 AC: 15506 AN: 67820

Other (OTH) AF: 0.174 AC: 368 AN: 2112

Alfa AF: 0.195 Hom.: 512

Bravo AF: 0.174

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.8
DANN	Benign	0.70
PhyloP100		1.9
Mutation Taster		=98/2	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: rs3917010; hg19: chr1-101190866;