rs4699824

Positions:

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

Variant summary

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

The ENST00000510657.1(EMCN):​n.282+14640C>T variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.363

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=-0.92).
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EMCN	ENST00000510657.1	n.282+14640C>T		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.318

Gnomad4 AMR AF: 0.659

Gnomad4 ASJ AF: 0.709

Gnomad4 EAS AF: 0.808

Gnomad4 SAS AF: 0.764

Gnomad4 FIN AF: 0.709

Gnomad4 NFE AF: 0.622

Gnomad4 OTH AF: 0.621

Alfa AF: 0.623 Hom.: 47395

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4699824; hg19: chr4-101722485;