rs1868463

Positions:

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000280481.9(FREM2):c.5003G>A(p.Arg1668His) variant causes a missense change. The variant allele was found at a frequency of 0.0623 in 1,603,678 control chromosomes in the GnomAD database, including 5,201 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.060 ( 434 hom., cov: 32)

Exomes 𝑓: 0.063 ( 4767 hom. )

Consequence

FREM2
ENST00000280481.9 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: 4.93

Variant links:

Genes affected

FREM2 (HGNC:25396): (FRAS1 related extracellular matrix 2) This gene encodes an integral membrane protein containing numerous CSPG (chondroitin sulfate proteoglycan element) repeats and Calx-beta domains. The encoded protein localizes to the basement membrane, forming a ternary complex that plays a role in epidermal-dermal interactions. This protein is important for the integrity of skin and renal epithelia. Mutations in this gene are associated with Fraser syndrome. [provided by RefSeq, Apr 2014]

FREM2 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=0.001679182).

BP6

Variant 13-38692347-G-A is Benign according to our data. Variant chr13-38692347-G-A is described in ClinVar as [Benign]. Clinvar id is 193534.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-38692347-G-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.227 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
FREM2	NM_207361.6 linkuse as main transcript	c.5003G>A	p.Arg1668His	missense_variant	1/24	ENST00000280481.9	NP_997244.4
FREM2	XM_017020554.2 linkuse as main transcript	c.5003G>A	p.Arg1668His	missense_variant	1/3		XP_016876043.1
FREM2	XR_941571.3 linkuse as main transcript	n.5271G>A		non_coding_transcript_exon_variant	1/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FREM2	ENST00000280481.9 linkuse as main transcript	c.5003G>A	p.Arg1668His	missense_variant	1/24	1	NM_207361.6	ENSP00000280481	P1	Q5SZK8-1

Frequencies

GnomAD3 genomes

AF:

0.0600

AC:

9115

AN:

152028

Hom.:

433

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0437

Gnomad AMI

AF:

0.0833

Gnomad AMR

AF:

0.0589

Gnomad ASJ

AF:

0.142

Gnomad EAS

AF:

0.239

Gnomad SAS

AF:

0.185

Gnomad FIN

AF:

0.0221

Gnomad MID

AF:

0.161

Gnomad NFE

AF:

0.0479

Gnomad OTH

AF:

0.0809

GnomAD3 exomes

AF:

0.0786

AC:

19187

AN:

244034

Hom.:

1319

AF XY:

0.0844

AC XY:

11117

AN XY:

131768

show subpopulations

Gnomad AFR exome

AF:

0.0434

Gnomad AMR exome

AF:

0.0366

Gnomad ASJ exome

AF:

0.146

Gnomad EAS exome

AF:

0.235

Gnomad SAS exome

AF:

0.179

Gnomad FIN exome

AF:

0.0185

Gnomad NFE exome

AF:

0.0505

Gnomad OTH exome

AF:

0.0756

GnomAD4 exome

AF:

0.0625

AC:

90777

AN:

1451532

Hom.:

4767

Cov.:

AF XY:

0.0666

AC XY:

48029

AN XY:

720976

show subpopulations

Gnomad4 AFR exome

AF:

0.0486

Gnomad4 AMR exome

AF:

0.0391

Gnomad4 ASJ exome

AF:

0.142

Gnomad4 EAS exome

AF:

0.262

Gnomad4 SAS exome

AF:

0.175

Gnomad4 FIN exome

AF:

0.0193

Gnomad4 NFE exome

AF:

0.0469

Gnomad4 OTH exome

AF:

0.0784

GnomAD4 genome

AF:

0.0599

AC:

9118

AN:

152146

Hom.:

434

Cov.:

AF XY:

0.0621

AC XY:

4621

AN XY:

74356

show subpopulations

Gnomad4 AFR

AF:

0.0436

Gnomad4 AMR

AF:

0.0589

Gnomad4 ASJ

AF:

0.142

Gnomad4 EAS

AF:

0.239

Gnomad4 SAS

AF:

0.185

Gnomad4 FIN

AF:

0.0221

Gnomad4 NFE

AF:

0.0479

Gnomad4 OTH

AF:

0.0852

Alfa

AF:

0.0593

Hom.:

1017

Bravo

AF:

0.0615

TwinsUK

AF:

0.0453

AC:

168

ALSPAC

AF:

0.0493

AC:

190

ESP6500AA

AF:

0.0431

AC:

190

ESP6500EA

AF:

0.0509

AC:

438

ExAC

AF:

0.0809

AC:

9816

Asia WGS

AF:

0.199

AC:

691

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 11, 2018	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -

not specified

Benign:2

Benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Nov 15, 2014	- -
Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -

Fraser syndrome 2

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.092

BayesDel_addAF

Benign

-0.55

BayesDel_noAF

Benign

-0.42

CADD

Pathogenic

DANN

Pathogenic

1.0

Eigen

Uncertain

0.59

Eigen_PC

Uncertain

0.54

FATHMM_MKL

Uncertain

0.95

MetaRNN

Benign

0.0017

MetaSVM

Benign

-1.1

MutationTaster

Benign

4.6e-7

PrimateAI

Benign

0.47

PROVEAN

Uncertain

-2.9

REVEL

Benign

0.21

Sift

Uncertain

0.0080

Sift4G

Uncertain

0.010

Vest4

0.24

MPC

0.53

ClinPred

0.022

GERP RS

4.5

gMVP

0.59

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