rs4699824

Variant names:

• chr4-100801328-G-A
• rs4699824
• ENST00000510657.1:n.282+14640C>T

Your query was ambiguous. Multiple possible variants found:

• chr4-100801328-G-A
• chr4-100801328-G-C

Variant summary

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

The ENST00000510657.1(EMCN):​n.282+14640C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 152,058 control chromosomes in the GnomAD database, including 26,014 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 0.56 (26014 hom., cov: 32)
• Consequence: EMCN ENST00000510657.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.363
• Publications: 5 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.787 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EMCN	ENST00000510657.1	n.282+14640C>T		intron_variant	Intron 3 of 5	4

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85463 AN: 151940 Hom.: 26010 Cov.: 32

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.625

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.808

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.709

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.618

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

GnomAD4 genome AF: 0.562 AC: 85475 AN: 152058 Hom.: 26014 Cov.: 32 AF XY: 0.574 AC XY: 42636 AN XY: 74332

African (AFR) AF: 0.318 AC: 13183 AN: 41462

American (AMR) AF: 0.659 AC: 10066 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.709 AC: 2462 AN: 3472

East Asian (EAS) AF: 0.808 AC: 4175 AN: 5170

South Asian (SAS) AF: 0.764 AC: 3677 AN: 4814

European-Finnish (FIN) AF: 0.709 AC: 7505 AN: 10578

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.622 AC: 42308 AN: 67978

Other (OTH) AF: 0.621 AC: 1311 AN: 2112

Alfa AF: 0.607 Hom.: 103432

Bravo AF: 0.546

Asia WGS AF: 0.733 AC: 2550 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.97
DANN	Benign	0.63
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs4699824; hg19: chr4-101722485;