4-100462475-T-C

Variant names:

• chr4-100462475-T-C
• rs357654
• NM_016242.4:c.376+2948A>G

Variant summary

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

The NM_016242.4(EMCN):​c.376+2948A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.818 in 152,098 control chromosomes in the GnomAD database, including 52,309 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 0.82 (52309 hom., cov: 32)
• Consequence: EMCN NM_016242.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0130
• 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:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.934 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EMCN	NM_016242.4	c.376+2948A>G		intron_variant	Intron 4 of 11	ENST00000296420.9	NP_057326.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EMCN	ENST00000296420.9	c.376+2948A>G		intron_variant	Intron 4 of 11	1	NM_016242.4	ENSP00000296420.4

Frequencies

GnomAD3 genomes AF: 0.818 AC: 124385 AN: 151980 Hom.: 52290 Cov.: 32

Gnomad AFR AF: 0.600

Gnomad AMI AF: 0.819

Gnomad AMR AF: 0.877

Gnomad ASJ AF: 0.903

Gnomad EAS AF: 0.917

Gnomad SAS AF: 0.956

Gnomad FIN AF: 0.933

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.897

Gnomad OTH AF: 0.848

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

GnomAD4 genome AF: 0.818 AC: 124441 AN: 152098 Hom.: 52309 Cov.: 32 AF XY: 0.824 AC XY: 61268 AN XY: 74370

African (AFR) AF: 0.600 AC: 24870 AN: 41456

American (AMR) AF: 0.877 AC: 13378 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.903 AC: 3134 AN: 3470

East Asian (EAS) AF: 0.917 AC: 4738 AN: 5166

South Asian (SAS) AF: 0.957 AC: 4618 AN: 4826

European-Finnish (FIN) AF: 0.933 AC: 9901 AN: 10610

Middle Eastern (MID) AF: 0.905 AC: 266 AN: 294

European-Non Finnish (NFE) AF: 0.897 AC: 61007 AN: 68004

Other (OTH) AF: 0.847 AC: 1784 AN: 2106

Alfa AF: 0.837 Hom.: 18145

Bravo AF: 0.801

Asia WGS AF: 0.914 AC: 3179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.1
DANN	Benign	0.80
PhyloP100		0.013
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: rs357654; hg19: chr4-101383632;