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GeneBe

4-100415923-G-A

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_016242.4(EMCN):c.726C>T(p.Thr242=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000736 in 1,587,032 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0043 ( 5 hom., cov: 32)
Exomes 𝑓: 0.00036 ( 1 hom. )

Consequence

EMCN
NM_016242.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.331
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.39).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 4-100415923-G-A is Benign according to our data. Variant chr4-100415923-G-A is described in ClinVar as [Benign]. Clinvar id is 790552.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0.331 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 5 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
EMCNNM_016242.4 linkuse as main transcriptc.726C>T p.Thr242= synonymous_variant 10/12 ENST00000296420.9
EMCNNM_001159694.2 linkuse as main transcriptc.687C>T p.Thr229= synonymous_variant 9/11
EMCNXM_011532024.4 linkuse as main transcriptc.726C>T p.Thr242= synonymous_variant 10/12

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
EMCNENST00000296420.9 linkuse as main transcriptc.726C>T p.Thr242= synonymous_variant 10/121 NM_016242.4 P1Q9ULC0-1
EMCNENST00000305864.7 linkuse as main transcriptc.477C>T p.Thr159= synonymous_variant 7/91 Q9ULC0-2
EMCNENST00000511970.5 linkuse as main transcriptc.687C>T p.Thr229= synonymous_variant 9/112 Q9ULC0-3
EMCNENST00000506300.5 linkuse as main transcriptc.197-5568C>T intron_variant 4

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00428
AC:
650
AN:
151738
Hom.:
5
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0151
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00118
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000736
Gnomad OTH
AF:
0.00144
GnomAD3 exomes
AF:
0.000993
AC:
224
AN:
225484
Hom.:
1
AF XY:
0.000655
AC XY:
80
AN XY:
122230
show subpopulations
Gnomad AFR exome
AF:
0.0142
Gnomad AMR exome
AF:
0.000421
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000405
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000379
Gnomad OTH exome
AF:
0.000372
GnomAD4 exome
AF:
0.000360
AC:
517
AN:
1435178
Hom.:
1
Cov.:
28
AF XY:
0.000328
AC XY:
234
AN XY:
713430
show subpopulations
Gnomad4 AFR exome
AF:
0.0139
Gnomad4 AMR exome
AF:
0.000530
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000498
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000127
Gnomad4 OTH exome
AF:
0.000674
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00429
AC:
651
AN:
151854
Hom.:
5
Cov.:
32
AF XY:
0.00411
AC XY:
305
AN XY:
74194
show subpopulations
Gnomad4 AFR
AF:
0.0151
Gnomad4 AMR
AF:
0.00118
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000736
Gnomad4 OTH
AF:
0.00142
Alfa
AF:
0.00197
Hom.:
2
Bravo
AF:
0.00472
Asia WGS
AF:
0.000867
AC:
3
AN:
3474

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeNov 14, 2017- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.39
Cadd
Benign
5.1
Dann
Benign
0.73

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs77192045; hg19: chr4-101337080; API