rs145754758

Variant names:

• chr8-98033137-C-A
• rs145754758
• NM_002380.5:c.2677C>A

Your query was ambiguous. Multiple possible variants found:

• chr8-98033137-C-A
• chr8-98033137-C-T

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2 BP4_Moderate BP7

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.486

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]

ACMG classification

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
MATN2	NM_002380.5	c.2677C>A	p.Arg893Arg	synonymous_variant	Exon 17 of 19	ENST00000254898.7	NP_002371.3
MATN2	NM_030583.4	c.2620C>A	p.Arg874Arg	synonymous_variant	Exon 17 of 19		NP_085072.2
MATN2	NM_001317748.2	c.2554C>A	p.Arg852Arg	synonymous_variant	Exon 16 of 18		NP_001304677.1
MATN2	XM_005250920.3	c.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
MATN2	ENST00000254898.7	c.2677C>A	p.Arg893Arg	synonymous_variant	Exon 17 of 19	1	NM_002380.5	ENSP00000254898.6
MATN2	ENST00000520016.5	c.2677C>A	p.Arg893Arg	synonymous_variant	Exon 16 of 18	1		ENSP00000430487.1
MATN2	ENST00000521689.5	c.2620C>A	p.Arg874Arg	synonymous_variant	Exon 17 of 19	1		ENSP00000429977.1
MATN2	ENST00000524308.5	c.2554C>A	p.Arg852Arg	synonymous_variant	Exon 16 of 18	1		ENSP00000430221.1
MATN2	ENST00000518154.5	c.1966C>A	p.Arg656Arg	synonymous_variant	Exon 14 of 16	1		ENSP00000429622.1
MATN2	ENST00000522025.6	c.1825C>A	p.Arg609Arg	synonymous_variant	Exon 16 of 18	5		ENSP00000429010.1
MATN2	ENST00000521952.5	n.*345C>A		non_coding_transcript_exon_variant	Exon 7 of 9	5		ENSP00000429256.1
MATN2	ENST00000521952.5	n.*345C>A		3_prime_UTR_variant	Exon 7 of 9	5		ENSP00000429256.1

Frequencies

GnomAD3 genomes AF: 0.00000657 AC: 1 AN: 152174 Hom.: 0 Cov.: 33

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

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

Other links and lift over

dbSNP: rs145754758; hg19: chr8-99045365;