Variant rs743920 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000334018.11(EMID1):c.326C>G(p.Ala109Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 1,613,198 control chromosomes in the GnomAD database, including 45,963 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.32 ( 12700 hom., cov: 34)

Exomes 𝑓: 0.17 ( 33263 hom. )

Consequence

EMID1
ENST00000334018.11 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.443

Variant links:

Genes affected

EMID1 (HGNC:18036): (EMI domain containing 1) Predicted to be located in several cellular components, including Golgi apparatus; endoplasmic reticulum; and extracellular matrix. Predicted to be part of collagen trimer. [provided by Alliance of Genome Resources, Apr 2022]

EMID1 links:

LOC105372985 (HGNC:):

LOC105372985 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EMID1	NM_133455.4 linkuse as main transcript	c.326C>G	p.Ala109Gly	missense_variant	4/15	ENST00000334018.11	NP_597712.2
LOC105372985	XR_001755481.2 linkuse as main transcript	n.100+592G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EMID1	ENST00000334018.11 linkuse as main transcript	c.326C>G	p.Ala109Gly	missense_variant	4/15	1	NM_133455.4	ENSP00000335481	P4	Q96A84-3

Frequencies

GnomAD3 genomes

AF:

0.321

AC:

48796

AN:

152086

Hom.:

12652

Cov.:

show subpopulations

Gnomad AFR

AF:

0.689

Gnomad AMI

AF:

0.0548

Gnomad AMR

AF:

0.305

Gnomad ASJ

AF:

0.197

Gnomad EAS

AF:

0.609

Gnomad SAS

AF:

0.323

Gnomad FIN

AF:

0.105

Gnomad MID

AF:

0.225

Gnomad NFE

AF:

0.123

Gnomad OTH

AF:

0.282

GnomAD3 exomes

AF:

0.254

AC:

63613

AN:

250888

Hom.:

12353

AF XY:

0.242

AC XY:

32832

AN XY:

135628

show subpopulations

Gnomad AFR exome

AF:

0.699

Gnomad AMR exome

AF:

0.344

Gnomad ASJ exome

AF:

0.195

Gnomad EAS exome

AF:

0.603

Gnomad SAS exome

AF:

0.311

Gnomad FIN exome

AF:

0.110

Gnomad NFE exome

AF:

0.125

Gnomad OTH exome

AF:

0.199

GnomAD4 exome

AF:

0.170

AC:

247885

AN:

1460994

Hom.:

33263

Cov.:

AF XY:

0.172

AC XY:

124658

AN XY:

726858

show subpopulations

Gnomad4 AFR exome

AF:

0.710

Gnomad4 AMR exome

AF:

0.340

Gnomad4 ASJ exome

AF:

0.200

Gnomad4 EAS exome

AF:

0.580

Gnomad4 SAS exome

AF:

0.310

Gnomad4 FIN exome

AF:

0.111

Gnomad4 NFE exome

AF:

0.121

Gnomad4 OTH exome

AF:

0.207

GnomAD4 genome

AF:

0.321

AC:

48904

AN:

152204

Hom.:

12700

Cov.:

AF XY:

0.321

AC XY:

23881

AN XY:

74426

show subpopulations

Gnomad4 AFR

AF:

0.690

Gnomad4 AMR

AF:

0.306

Gnomad4 ASJ

AF:

0.197

Gnomad4 EAS

AF:

0.609

Gnomad4 SAS

AF:

0.322

Gnomad4 FIN

AF:

0.105

Gnomad4 NFE

AF:

0.123

Gnomad4 OTH

AF:

0.288

Alfa

AF:

0.134

Hom.:

641

Bravo

AF:

0.351

TwinsUK

AF:

0.119

AC:

441

ALSPAC

AF:

0.112

AC:

430

ESP6500AA

AF:

0.679

AC:

2990

ESP6500EA

AF:

0.129

AC:

1108

ExAC

AF:

0.256

AC:

31053

Asia WGS

AF:

0.454

AC:

1578

AN:

3478

EpiCase

AF:

0.124

EpiControl

AF:

0.131

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.60

BayesDel_noAF

Benign

-0.49

CADD

Benign

DANN

Benign

0.10

DEOGEN2

Benign

0.0024

.;T;T;T

Eigen

Benign

-1.5

Eigen_PC

Benign

-1.3

FATHMM_MKL

Benign

0.013

LIST_S2

Benign

0.093

T;T;T;T

MetaRNN

Benign

0.0000028

T;T;T;T

MetaSVM

Benign

-0.95

MutationTaster

Benign

1.0

P;P;P

PrimateAI

Benign

0.32

PROVEAN

Benign

1.5

N;N;N;N

REVEL

Benign

0.13

Sift

Benign

1.0

T;T;T;T

Sift4G

Benign

1.0

T;T;T;T

Polyphen

0.0

B;.;B;B

Vest4

0.092

MPC

0.12

ClinPred

0.000011

GERP RS

1.3

gMVP

0.23

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.35

Details are displayed if max score is > 0.2

DS_AG_spliceai

0.35

Position offset: 0

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over