NM_002380.5:c.2677C>A

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7

The NM_002380.5(MATN2):​c.2677C>A​(p.Arg893Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,174 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0000066 ( 0 hom., cov: 33)

Consequence

MATN2
NM_002380.5 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.486
Variant links:
Genes affected
MATN2 (HGNC:6908): (matrilin 2) This gene encodes a member of the von Willebrand factor A domain containing protein family. This family of proteins is thought to be involved in the formation of filamentous networks in the extracellular matrices of various tissues. This protein contains five von Willebrand factor A domains. The specific function of this gene has not yet been determined. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
RPL30 (HGNC:10333): (ribosomal protein L30) Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein that is a component of the 60S subunit. The protein belongs to the L30E family of ribosomal proteins. It is located in the cytoplasm. This gene is co-transcribed with the U72 small nucleolar RNA gene, which is located in its fourth intron. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.23).
BP7
Synonymous conserved (PhyloP=0.486 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MATN2NM_002380.5 linkc.2677C>A p.Arg893Arg synonymous_variant Exon 17 of 19 ENST00000254898.7 NP_002371.3 O00339-1A0A140VKH7Q8N2G3
MATN2NM_030583.4 linkc.2620C>A p.Arg874Arg synonymous_variant Exon 17 of 19 NP_085072.2 O00339-2Q8N2G3
MATN2NM_001317748.2 linkc.2554C>A p.Arg852Arg synonymous_variant Exon 16 of 18 NP_001304677.1 O00339-3Q8N2G3
MATN2XM_005250920.3 linkc.2263C>A p.Arg755Arg synonymous_variant Exon 16 of 18 XP_005250977.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MATN2ENST00000254898.7 linkc.2677C>A p.Arg893Arg synonymous_variant Exon 17 of 19 1 NM_002380.5 ENSP00000254898.6 O00339-1
MATN2ENST00000520016.5 linkc.2677C>A p.Arg893Arg synonymous_variant Exon 16 of 18 1 ENSP00000430487.1 O00339-1
MATN2ENST00000521689.5 linkc.2620C>A p.Arg874Arg synonymous_variant Exon 17 of 19 1 ENSP00000429977.1 O00339-2
MATN2ENST00000524308.5 linkc.2554C>A p.Arg852Arg synonymous_variant Exon 16 of 18 1 ENSP00000430221.1 O00339-3
MATN2ENST00000518154.5 linkc.1966C>A p.Arg656Arg synonymous_variant Exon 14 of 16 1 ENSP00000429622.1 H0YBJ4
MATN2ENST00000522025.6 linkc.1825C>A p.Arg609Arg synonymous_variant Exon 16 of 18 5 ENSP00000429010.1 O00339-4
MATN2ENST00000521952.5 linkn.*345C>A non_coding_transcript_exon_variant Exon 7 of 9 5 ENSP00000429256.1 H0YBD5
MATN2ENST00000521952.5 linkn.*345C>A 3_prime_UTR_variant Exon 7 of 9 5 ENSP00000429256.1 H0YBD5

Frequencies

GnomAD3 genomes
AF:
0.00000657
AC:
1
AN:
152174
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000147
Gnomad OTH
AF:
0.00
GnomAD4 exome
Cov.:
31
GnomAD4 genome
AF:
0.00000657
AC:
1
AN:
152174
Hom.:
0
Cov.:
33
AF XY:
0.00
AC XY:
0
AN XY:
74348
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000147
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.23
CADD
Benign
7.9
DANN
Benign
0.82

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
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.

Other links and lift over

dbSNP: rs145754758; hg19: chr8-99045365; API