rs3775369

Positions:

• chr4-100512097-G-A

Variant summary

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

The NM_016242.4(EMCN):​c.64+5754C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.041 in 152,216 control chromosomes in the GnomAD database, including 307 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 0.041 (307 hom., cov: 32)
• Consequence: EMCN NM_016242.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.431

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EMCN	NM_016242.4	c.64+5754C>T		intron_variant		ENST00000296420.9
EMCN	NM_001159694.2	c.64+5754C>T		intron_variant
EMCN	XM_011532024.4	c.64+5754C>T		intron_variant
EMCN	XM_017008290.2	c.64+5754C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EMCN	ENST00000296420.9	c.64+5754C>T		intron_variant		1	NM_016242.4	P1

Frequencies

GnomAD3 genomes AF: 0.0409 AC: 6228 AN: 152098 Hom.: 307 Cov.: 32

Gnomad AFR AF: 0.0520

Gnomad AMI AF: 0.00549

Gnomad AMR AF: 0.0248

Gnomad ASJ AF: 0.00490

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.0768

Gnomad FIN AF: 0.0510

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0202

Gnomad OTH AF: 0.0397

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

GnomAD4 genome AF: 0.0410 AC: 6237 AN: 152216 Hom.: 307 Cov.: 32 AF XY: 0.0435 AC XY: 3240 AN XY: 74416

Gnomad4 AFR AF: 0.0519

Gnomad4 AMR AF: 0.0247

Gnomad4 ASJ AF: 0.00490

Gnomad4 EAS AF: 0.254

Gnomad4 SAS AF: 0.0769

Gnomad4 FIN AF: 0.0510

Gnomad4 NFE AF: 0.0201

Gnomad4 OTH AF: 0.0407

Alfa AF: 0.0311 Hom.: 17

Bravo AF: 0.0401

Asia WGS AF: 0.158 AC: 552 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.7
DANN	Benign	0.63

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

Publications

LitVar

Other links and lift over

dbSNP: rs3775369; hg19: chr4-101433254;