rs357663

Variant names:

• chr4-100469948-T-G
• rs357663
• NM_016242.4:c.260-4409A>C

Variant summary

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

The NM_016242.4(EMCN):​c.260-4409A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 151,776 control chromosomes in the GnomAD database, including 14,618 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 0.39 (14618 hom., cov: 32)
• Consequence: EMCN NM_016242.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• Publications: 2 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]

ENSG00000286150 (HGNC:):

ENSG00000294250 (HGNC:58859):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016242.4. 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
	EMCN	NM_016242.4	MANE Select	c.260-4409A>C		intron	N/A	NP_057326.2
	EMCN	NM_001159694.2		c.260-4409A>C		intron	N/A	NP_001153166.1	Q9ULC0-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EMCN	ENST00000296420.9	TSL:1 MANE Select	c.260-4409A>C		intron	N/A	ENSP00000296420.4	Q9ULC0-1
	EMCN	ENST00000305864.7	TSL:1	c.260-4409A>C		intron	N/A	ENSP00000304780.3	Q9ULC0-2
	EMCN	ENST00000956441.1		c.260-4409A>C		intron	N/A	ENSP00000626500.1

Frequencies

GnomAD3 genomes AF: 0.395 AC: 59945 AN: 151658 Hom.: 14624 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.395 AC: 59935 AN: 151776 Hom.: 14618 Cov.: 32 AF XY: 0.390 AC XY: 28913 AN XY: 74178

African (AFR) AF: 0.133 AC: 5526 AN: 41446

American (AMR) AF: 0.326 AC: 4976 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 1705 AN: 3462

East Asian (EAS) AF: 0.140 AC: 726 AN: 5176

South Asian (SAS) AF: 0.403 AC: 1940 AN: 4816

European-Finnish (FIN) AF: 0.521 AC: 5486 AN: 10530

Middle Eastern (MID) AF: 0.490 AC: 140 AN: 286

European-Non Finnish (NFE) AF: 0.561 AC: 38030 AN: 67788

Other (OTH) AF: 0.417 AC: 878 AN: 2104

Alfa AF: 0.467 Hom.: 2322

Bravo AF: 0.364

Asia WGS AF: 0.291 AC: 1011 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	8.8
DANN	Benign	0.88
PhyloP100		0.21
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs357663; hg19: chr4-101391105;