rs11725047

Positions:

• chr4-100877640-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000510657.1(EMCN):​n.123+2364T>G variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.313

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EMCN	ENST00000510657.1	n.123+2364T>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.0482

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.0879

Gnomad4 EAS AF: 0.0990

Gnomad4 SAS AF: 0.0381

Gnomad4 FIN AF: 0.120

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.110

Alfa AF: 0.114 Hom.: 1434

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11725047; hg19: chr4-101798797;