chr4-100397108-C-T

Variant names:

• chr4-100397108-C-T
• rs3087542
• NM_016242.4:c.*1305G>A

Variant summary

Our verdict is Benign. The variant received -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
• 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=-0.81).
• 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 rank	MANE	Protein	UniProt
EMCN	NM_016242.4	c.*1305G>A		3_prime_UTR_variant	Exon 12 of 12	ENST00000296420.9	NP_057326.2
EMCN	NM_001159694.2	c.*1305G>A		3_prime_UTR_variant	Exon 11 of 11		NP_001153166.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EMCN	ENST00000296420.9	c.*1305G>A		3_prime_UTR_variant	Exon 12 of 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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.168 AC: 6966 AN: 41468

American (AMR) AF: 0.328 AC: 4997 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.0991 AC: 344 AN: 3470

East Asian (EAS) AF: 0.770 AC: 3954 AN: 5138

South Asian (SAS) AF: 0.306 AC: 1470 AN: 4808

European-Finnish (FIN) AF: 0.147 AC: 1554 AN: 10554

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0974 AC: 6619 AN: 67968

Other (OTH) AF: 0.164 AC: 347 AN: 2110

Alfa AF: 0.144 Hom.: 836

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
PhyloP100		-1.0
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: rs3087542; hg19: chr4-101318265;