dbSNP rs1065755: MATN1:p.Glu425Glu (chr1-30715242-C-T) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_002379.3(MATN1):c.1275G>A(p.Glu425Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.345 in 1,613,812 control chromosomes in the GnomAD database, including 98,059 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.33 ( 8315 hom., cov: 33)

Exomes 𝑓: 0.35 ( 89744 hom. )

Consequence

MATN1
NM_002379.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0810

Publications

17 publications found

Variant links:

Genes affected

MATN1 (HGNC:6907): (matrilin 1) This gene encodes a member of von Willebrand factor A domain containing protein family. This family of proteins are thought to be involved in the formation of filamentous networks in the extracellular matrices of various tissues. Mutations of this gene have been associated with variety of inherited chondrodysplasias. [provided by RefSeq, Jul 2008]

MATN1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.57).

BP7

Synonymous conserved (PhyloP=-0.081 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MATN1	NM_002379.3 link	c.1275G>A	p.Glu425Glu	synonymous_variant	Exon 6 of 8	ENST00000373765.5	NP_002370.1	P21941

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MATN1	ENST00000373765.5 link	c.1275G>A	p.Glu425Glu	synonymous_variant	Exon 6 of 8	1	NM_002379.3	ENSP00000362870.4		P21941
MATN1	ENST00000494561.1 link	n.295G>A		non_coding_transcript_exon_variant	Exon 2 of 3	3

Frequencies

GnomAD3 genomes

AF:

0.327

AC:

49679

AN:

152062

Hom.:

8308

Cov.:

show subpopulations

Gnomad AFR

AF:

0.283

Gnomad AMI

AF:

0.346

Gnomad AMR

AF:

0.359

Gnomad ASJ

AF:

0.283

Gnomad EAS

AF:

0.180

Gnomad SAS

AF:

0.268

Gnomad FIN

AF:

0.426

Gnomad MID

AF:

0.269

Gnomad NFE

AF:

0.348

Gnomad OTH

AF:

0.327

GnomAD2 exomes

AF:

0.332

AC:

83345

AN:

251412

AF XY:

0.326

show subpopulations

Gnomad AFR exome

AF:

0.283

Gnomad AMR exome

AF:

0.408

Gnomad ASJ exome

AF:

0.277

Gnomad EAS exome

AF:

0.166

Gnomad FIN exome

AF:

0.421

Gnomad NFE exome

AF:

0.342

Gnomad OTH exome

AF:

0.326

GnomAD4 exome

AF:

0.347

AC:

507516

AN:

1461632

Hom.:

89744

Cov.:

AF XY:

0.344

AC XY:

250480

AN XY:

727118

show subpopulations

African (AFR)

AF:

0.282

AC:

9437

AN:

33476

American (AMR)

AF:

0.405

AC:

18131

AN:

44714

Ashkenazi Jewish (ASJ)

AF:

0.277

AC:

7234

AN:

26132

East Asian (EAS)

AF:

0.234

AC:

9286

AN:

39696

South Asian (SAS)

AF:

0.286

AC:

24695

AN:

86248

European-Finnish (FIN)

AF:

0.415

AC:

22142

AN:

53408

Middle Eastern (MID)

AF:

0.251

AC:

1450

AN:

5768

European-Non Finnish (NFE)

AF:

0.356

AC:

395397

AN:

1111806

Other (OTH)

AF:

0.327

AC:

19744

AN:

60384

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.469

Heterozygous variant carriers

17221

34442

51664

68885

86106

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

12572

25144

37716

50288

62860

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.327

AC:

49721

AN:

152180

Hom.:

8315

Cov.:

AF XY:

0.326

AC XY:

24224

AN XY:

74404

show subpopulations

African (AFR)

AF:

0.283

AC:

11754

AN:

41510

American (AMR)

AF:

0.359

AC:

5494

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.283

AC:

982

AN:

3470

East Asian (EAS)

AF:

0.180

AC:

932

AN:

5174

South Asian (SAS)

AF:

0.268

AC:

1296

AN:

4828

European-Finnish (FIN)

AF:

0.426

AC:

4504

AN:

10578

Middle Eastern (MID)

AF:

0.269

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.348

AC:

23678

AN:

68008

Other (OTH)

AF:

0.325

AC:

687

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1762

3523

5285

7046

8808

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

492

984

1476

1968

2460

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.334

Hom.:

4710

Bravo

AF:

0.320

Asia WGS

AF:

0.231

AC:

803

AN:

3478

EpiCase

AF:

0.331

EpiControl

AF:

0.327

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.57

CADD

Benign

5.1

(source)

DANN

Benign

0.69

PhyloP100

-0.081

Mutation Taster

=99/1

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over