4-100527843-T-G

Variant names:

• chr4-100527843-T-G
• rs357671
• ENST00000510657.1:n.503+42361A>C

Variant summary

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

The ENST00000510657.1(EMCN):​n.503+42361A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 152,138 control chromosomes in the GnomAD database, including 4,204 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 0.21 (4204 hom., cov: 31)
• Consequence: EMCN ENST00000510657.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.206
• Publications: 0 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000510657.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EMCN	ENST00000510657.1	TSL:4	n.503+42361A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31873 AN: 152020 Hom.: 4201 Cov.: 31

Gnomad AFR AF: 0.0538

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.210 AC: 31875 AN: 152138 Hom.: 4204 Cov.: 31 AF XY: 0.208 AC XY: 15502 AN XY: 74378

African (AFR) AF: 0.0536 AC: 2226 AN: 41548

American (AMR) AF: 0.181 AC: 2762 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.224 AC: 776 AN: 3468

East Asian (EAS) AF: 0.174 AC: 899 AN: 5170

South Asian (SAS) AF: 0.232 AC: 1120 AN: 4824

European-Finnish (FIN) AF: 0.285 AC: 3012 AN: 10582

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.300 AC: 20413 AN: 67968

Other (OTH) AF: 0.221 AC: 467 AN: 2110

Alfa AF: 0.256 Hom.: 709

Bravo AF: 0.192

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.4
DANN	Benign	0.46
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs357671; hg19: chr4-101449000;