rs1392874

Variant names:

• chr4-100545663-C-A
• rs1392874
• ENST00000510657.1:n.503+24541G>T

Variant summary

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

The ENST00000510657.1(EMCN):​n.503+24541G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 152,078 control chromosomes in the GnomAD database, including 13,244 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 0.41 (13244 hom., cov: 32)
• Consequence: EMCN ENST00000510657.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.437
• Publications: 5 publications found

Genes affected

EMCN (HGNC:16041): (endomucin) EMCN is a mucin-like sialoglycoprotein that interferes with the assembly of focal adhesion complexes and inhibits interaction between cells and the extracellular matrix (Kinoshita et al., 2001 [PubMed 11418125]).[supplied by OMIM, Mar 2008]

LOC105377345 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000510657.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EMCN	ENST00000510657.1	TSL:4	n.503+24541G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62753 AN: 151960 Hom.: 13215 Cov.: 32

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.413 AC: 62824 AN: 152078 Hom.: 13244 Cov.: 32 AF XY: 0.409 AC XY: 30387 AN XY: 74322

African (AFR) AF: 0.492 AC: 20422 AN: 41468

American (AMR) AF: 0.351 AC: 5367 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1093 AN: 3468

East Asian (EAS) AF: 0.263 AC: 1359 AN: 5160

South Asian (SAS) AF: 0.326 AC: 1572 AN: 4822

European-Finnish (FIN) AF: 0.418 AC: 4413 AN: 10546

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.401 AC: 27252 AN: 68002

Other (OTH) AF: 0.418 AC: 883 AN: 2114

Alfa AF: 0.402 Hom.: 21659

Bravo AF: 0.412

Asia WGS AF: 0.316 AC: 1102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.4
DANN	Benign	0.68
PhyloP100		0.44

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1392874;

hg19: chr4-101466820;