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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377345	XR_939023.3	n.386-322C>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EMCN	ENST00000510657.1	n.503+24541G>T		intron_variant	Intron 5 of 5	4

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 v4.3

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

Other links and lift over

dbSNP: rs1392874; hg19: chr4-101466820;