rs151102225

Positions:

chr1-150512368-A-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The ENST00000369047.9(ECM1):c.1100A>T(p.Asp367Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00987 in 1,612,804 control chromosomes in the GnomAD database, including 99 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0073 ( 7 hom., cov: 27)

Exomes 𝑓: 0.010 ( 92 hom. )

Consequence

ECM1
ENST00000369047.9 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: 2.59

Variant links:

Genes affected

ECM1 (HGNC:3153): (extracellular matrix protein 1) This gene encodes a soluble protein that is involved in endochondral bone formation, angiogenesis, and tumor biology. It also interacts with a variety of extracellular and structural proteins, contributing to the maintenance of skin integrity and homeostasis. Mutations in this gene are associated with lipoid proteinosis disorder (also known as hyalinosis cutis et mucosae or Urbach-Wiethe disease) that is characterized by generalized thickening of skin, mucosae and certain viscera. Alternatively spliced transcript variants encoding distinct isoforms have been described for this gene. [provided by RefSeq, Feb 2011]

ECM1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.015558243).

BP6

Variant 1-150512368-A-T is Benign according to our data. Variant chr1-150512368-A-T is described in ClinVar as [Likely_benign]. Clinvar id is 376771.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00728 (1098/150920) while in subpopulation NFE AF= 0.0117 (792/67776). AF 95% confidence interval is 0.011. There are 7 homozygotes in gnomad4. There are 528 alleles in male gnomad4 subpopulation. Median coverage is 27. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 7 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
ECM1	NM_004425.4 linkuse as main transcript	c.1100A>T	p.Asp367Val	missense_variant	8/10	ENST00000369047.9	NP_004416.2
ECM1	NM_001202858.2 linkuse as main transcript	c.1181A>T	p.Asp394Val	missense_variant	8/10		NP_001189787.1
ECM1	NM_022664.3 linkuse as main transcript	c.725A>T	p.Asp242Val	missense_variant	7/9		NP_073155.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ECM1	ENST00000369047.9 linkuse as main transcript	c.1100A>T	p.Asp367Val	missense_variant	8/10	1	NM_004425.4	ENSP00000358043	P1	Q16610-1
ECM1	ENST00000346569.6 linkuse as main transcript	c.725A>T	p.Asp242Val	missense_variant	7/9	1		ENSP00000271630		Q16610-2
ECM1	ENST00000369049.8 linkuse as main transcript	c.1181A>T	p.Asp394Val	missense_variant	8/10	2		ENSP00000358045		Q16610-4
ECM1	ENST00000470432.5 linkuse as main transcript	n.2457A>T		non_coding_transcript_exon_variant	4/6	2

Frequencies

GnomAD3 genomes

AF:

0.00729

AC:

1099

AN:

150802

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00203

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00612

Gnomad ASJ

AF:

0.0159

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00468

Gnomad FIN

AF:

0.00460

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0117

Gnomad OTH

AF:

0.00338

GnomAD3 exomes

AF:

0.00729

AC:

1828

AN:

250644

Hom.:

AF XY:

0.00749

AC XY:

1016

AN XY:

135564

show subpopulations

Gnomad AFR exome

AF:

0.00197

Gnomad AMR exome

AF:

0.00332

Gnomad ASJ exome

AF:

0.0138

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00578

Gnomad FIN exome

AF:

0.00504

Gnomad NFE exome

AF:

0.0107

Gnomad OTH exome

AF:

0.00782

GnomAD4 exome

AF:

0.0101

AC:

14825

AN:

1461884

Hom.:

Cov.:

AF XY:

0.00993

AC XY:

7221

AN XY:

727244

show subpopulations

Gnomad4 AFR exome

AF:

0.00143

Gnomad4 AMR exome

AF:

0.00349

Gnomad4 ASJ exome

AF:

0.0160

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00599

Gnomad4 FIN exome

AF:

0.00603

Gnomad4 NFE exome

AF:

0.0115

Gnomad4 OTH exome

AF:

0.00911

GnomAD4 genome

AF:

0.00728

AC:

1098

AN:

150920

Hom.:

Cov.:

AF XY:

0.00717

AC XY:

528

AN XY:

73632

show subpopulations

Gnomad4 AFR

AF:

0.00202

Gnomad4 AMR

AF:

0.00605

Gnomad4 ASJ

AF:

0.0159

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00468

Gnomad4 FIN

AF:

0.00460

Gnomad4 NFE

AF:

0.0117

Gnomad4 OTH

AF:

0.00334

Alfa

AF:

0.00943

Hom.:

Bravo

AF:

0.00651

TwinsUK

AF:

0.0132

AC:

ALSPAC

AF:

0.0143

AC:

ESP6500AA

AF:

0.00250

AC:

ESP6500EA

AF:

0.0109

AC:

ExAC

AF:

0.00773

AC:

939

Asia WGS

AF:

0.00173

AC:

AN:

3478

EpiCase

AF:

0.00862

EpiControl

AF:

0.00925

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:4

Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Likely benign, criteria provided, single submitter	clinical testing	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	Dec 30, 2016	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 31, 2019	- -
Benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Feb 01, 2024	ECM1: BS1, BS2 -

Lipid proteinosis

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Apr 11, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.82

BayesDel_addAF

Benign

-0.25

BayesDel_noAF

Benign

-0.12

CADD

Uncertain

DANN

Uncertain

0.99

DEOGEN2

Uncertain

0.56

.;D;.

Eigen

Uncertain

0.42

Eigen_PC

Uncertain

0.32

FATHMM_MKL

Uncertain

0.77

LIST_S2

Uncertain

0.90

D;D;D

MetaRNN

Benign

0.016

T;T;T

MetaSVM

Uncertain

-0.084

MutationAssessor

Uncertain

2.3

.;M;.

MutationTaster

Benign

1.0

D;D;N

PrimateAI

Benign

0.43

PROVEAN

Pathogenic

-7.4

D;D;D

REVEL

Uncertain

0.58

Sift

Uncertain

0.0010

D;D;D

Sift4G

Pathogenic

0.0

D;D;D

Polyphen

1.0

D;D;D

Vest4

0.64

MVP

0.95

MPC

0.62

ClinPred

0.032

GERP RS

4.6

Varity_R

0.67

gMVP

0.75

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over