dbSNP rs2233107: MATN4:c.*4C>T (chr20-45293763-G-A) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_001393530.1(MATN4):c.*4C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0405 in 1,605,244 control chromosomes in the GnomAD database, including 3,037 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.077 ( 761 hom., cov: 32)

Exomes 𝑓: 0.037 ( 2276 hom. )

Consequence

MATN4
NM_001393530.1 3_prime_UTR

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.00300

Variant links:

Genes affected

MATN4 (HGNC:6910): (matrilin 4) This gene encodes a member of von Willebrand factor A domain-containing protein family. The proteins of this family are thought to be involved in the formation of filamentous networks in the extracellular matrices of various tissues. This family member is thought to be play a role in reorganizing and regenerating the corneal matrix in granular and lattice type I dystrophies. It may also be involved in wound healing in the dentin-pulp complex. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2013]

MATN4 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.67).

BP6

Variant 20-45293763-G-A is Benign according to our data. Variant chr20-45293763-G-A is described in ClinVar as [Benign]. Clinvar id is 3059206.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MATN4	NM_001393530.1 link	c.*4C>T		3_prime_UTR_variant	Exon 10 of 10	ENST00000372756.6	NP_001380459.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
MATN4	ENST00000372756 link	c.*4C>T	3_prime_UTR_variant	Exon 10 of 10	1	NM_001393530.1	ENSP00000361842.1	O95460-2
MATN4	ENST00000372754 link	c.*4C>T	3_prime_UTR_variant	Exon 10 of 10	5		ENSP00000361840.1	O95460-1
MATN4	ENST00000360607 link	c.*4C>T	3_prime_UTR_variant	Exon 9 of 9	1		ENSP00000353819.5	O95460-4

Frequencies

GnomAD3 genomes

AF:

0.0766

AC:

11658

AN:

152162

Hom.:

752

Cov.:

show subpopulations

Gnomad AFR

AF:

0.140

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.171

Gnomad ASJ

AF:

0.0135

Gnomad EAS

AF:

0.0754

Gnomad SAS

AF:

0.0269

Gnomad FIN

AF:

0.0840

Gnomad MID

AF:

0.0159

Gnomad NFE

AF:

0.0242

Gnomad OTH

AF:

0.0712

GnomAD3 exomes

AF:

0.0689

AC:

16468

AN:

238906

Hom.:

1175

AF XY:

0.0593

AC XY:

7745

AN XY:

130536

show subpopulations

Gnomad AFR exome

AF:

0.140

Gnomad AMR exome

AF:

0.217

Gnomad ASJ exome

AF:

0.0199

Gnomad EAS exome

AF:

0.0791

Gnomad SAS exome

AF:

0.0273

Gnomad FIN exome

AF:

0.0824

Gnomad NFE exome

AF:

0.0257

Gnomad OTH exome

AF:

0.0614

GnomAD4 exome

AF:

0.0367

AC:

53252

AN:

1452964

Hom.:

2276

Cov.:

AF XY:

0.0352

AC XY:

25430

AN XY:

722942

show subpopulations

Gnomad4 AFR exome

AF:

0.144

Gnomad4 AMR exome

AF:

0.215

Gnomad4 ASJ exome

AF:

0.0184

Gnomad4 EAS exome

AF:

0.0702

Gnomad4 SAS exome

AF:

0.0287

Gnomad4 FIN exome

AF:

0.0818

Gnomad4 NFE exome

AF:

0.0238

Gnomad4 OTH exome

AF:

0.0444

GnomAD4 genome

AF:

0.0768

AC:

11695

AN:

152280

Hom.:

761

Cov.:

AF XY:

0.0811

AC XY:

6038

AN XY:

74464

show subpopulations

Gnomad4 AFR

AF:

0.140

Gnomad4 AMR

AF:

0.171

Gnomad4 ASJ

AF:

0.0135

Gnomad4 EAS

AF:

0.0752

Gnomad4 SAS

AF:

0.0269

Gnomad4 FIN

AF:

0.0840

Gnomad4 NFE

AF:

0.0242

Gnomad4 OTH

AF:

0.0699

Alfa

AF:

0.0376

Hom.:

154

Bravo

AF:

0.0880

Asia WGS

AF:

0.0470

AC:

165

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

MATN4-related disorder

Benign:1

Oct 28, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

9.0

DANN

Benign

0.95

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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