rs11725047

Variant names:

• chr4-100877640-A-C
• rs11725047
• ENST00000510657.1:n.123+2364T>G

Variant summary

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

The ENST00000510657.1(EMCN):​n.123+2364T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0972 in 152,040 control chromosomes in the GnomAD database, including 834 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 0.097 (834 hom., cov: 32)
• Consequence: EMCN ENST00000510657.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.313
• Publications: 4 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]

LINC01218 (HGNC:41420): (long intergenic non-protein coding RNA 1218)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01218	NR_189167.1	n.119+2364T>G		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EMCN	ENST00000510657.1	n.123+2364T>G		intron_variant	Intron 1 of 5	4

Frequencies

GnomAD3 genomes AF: 0.0973 AC: 14778 AN: 151922 Hom.: 834 Cov.: 32

Gnomad AFR AF: 0.0484

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0879

Gnomad EAS AF: 0.0992

Gnomad SAS AF: 0.0383

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.0972 AC: 14774 AN: 152040 Hom.: 834 Cov.: 32 AF XY: 0.0954 AC XY: 7091 AN XY: 74318

African (AFR) AF: 0.0482 AC: 2001 AN: 41528

American (AMR) AF: 0.105 AC: 1607 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.0879 AC: 305 AN: 3468

East Asian (EAS) AF: 0.0990 AC: 510 AN: 5150

South Asian (SAS) AF: 0.0381 AC: 184 AN: 4826

European-Finnish (FIN) AF: 0.120 AC: 1267 AN: 10586

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8495 AN: 67928

Other (OTH) AF: 0.110 AC: 231 AN: 2108

Alfa AF: 0.112 Hom.: 1917

Bravo AF: 0.0940

Asia WGS AF: 0.0840 AC: 291 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.1
DANN	Benign	0.55
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs11725047; hg19: chr4-101798797;