chr4-100397108-C-T

Position:

• chr4-100397108-C-T

Variant summary

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

The NM_016242.4(EMCN):​c.*1305G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 151,964 control chromosomes in the GnomAD database, including 3,810 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 0.17 (3810 hom., cov: 31)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: EMCN NM_016242.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.75 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EMCN	NM_016242.4	c.*1305G>A		3_prime_UTR_variant	12/12	ENST00000296420.9	NP_057326.2
EMCN	NM_001159694.2	c.*1305G>A		3_prime_UTR_variant	11/11		NP_001153166.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EMCN	ENST00000296420.9	c.*1305G>A		3_prime_UTR_variant	12/12	1	NM_016242.4	ENSP00000296420.4

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26315 AN: 151844 Hom.: 3800 Cov.: 31

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.0991

Gnomad EAS AF: 0.769

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0974

Gnomad OTH AF: 0.163

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.173 AC: 26343 AN: 151962 Hom.: 3810 Cov.: 31 AF XY: 0.184 AC XY: 13702 AN XY: 74280

Gnomad4 AFR AF: 0.168

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.0991

Gnomad4 EAS AF: 0.770

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.0974

Gnomad4 OTH AF: 0.164

Alfa AF: 0.160 Hom.: 547

Bravo AF: 0.191

Asia WGS AF: 0.492 AC: 1710 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.4
DANN	Benign	0.60

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

Publications

LitVar

Other links and lift over

dbSNP: rs3087542; hg19: chr4-101318265;