chr8-97926160-C-T

Variant names:

• chr8-97926160-C-T
• rs1378124
• NM_002380.5:c.143-4793C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002380.5(MATN2):​c.143-4793C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.654 in 151,890 control chromosomes in the GnomAD database, including 33,207 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 0.65 (33207 hom., cov: 31)
• Consequence: MATN2 NM_002380.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.630
• Publications: 4 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.9 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MATN2	NM_002380.5	c.143-4793C>T		intron_variant	Intron 2 of 18	ENST00000254898.7	NP_002371.3
MATN2	NM_030583.4	c.143-4793C>T		intron_variant	Intron 2 of 18		NP_085072.2
MATN2	NM_001317748.2	c.143-4793C>T		intron_variant	Intron 2 of 17		NP_001304677.1
MATN2	XM_005250920.3	c.143-4793C>T		intron_variant	Intron 2 of 17		XP_005250977.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MATN2	ENST00000254898.7	c.143-4793C>T		intron_variant	Intron 2 of 18	1	NM_002380.5	ENSP00000254898.6
MATN2	ENST00000520016.5	c.143-4793C>T		intron_variant	Intron 1 of 17	1		ENSP00000430487.1
MATN2	ENST00000521689.5	c.143-4793C>T		intron_variant	Intron 2 of 18	1		ENSP00000429977.1
MATN2	ENST00000524308.5	c.143-4793C>T		intron_variant	Intron 2 of 17	1		ENSP00000430221.1
MATN2	ENST00000522025.6	c.-117-4378C>T		intron_variant	Intron 1 of 17	5		ENSP00000429010.1

Frequencies

GnomAD3 genomes AF: 0.654 AC: 99295 AN: 151772 Hom.: 33186 Cov.: 31

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.742

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.922

Gnomad SAS AF: 0.820

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.654

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.654 AC: 99365 AN: 151890 Hom.: 33207 Cov.: 31 AF XY: 0.660 AC XY: 48990 AN XY: 74238

African (AFR) AF: 0.544 AC: 22508 AN: 41402

American (AMR) AF: 0.743 AC: 11337 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.699 AC: 2424 AN: 3470

East Asian (EAS) AF: 0.922 AC: 4749 AN: 5150

South Asian (SAS) AF: 0.821 AC: 3953 AN: 4814

European-Finnish (FIN) AF: 0.623 AC: 6547 AN: 10516

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.675 AC: 45846 AN: 67956

Other (OTH) AF: 0.658 AC: 1390 AN: 2112

Alfa AF: 0.672 Hom.: 131764

Bravo AF: 0.656

Asia WGS AF: 0.839 AC: 2918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	6.3
DANN	Benign	0.80
PhyloP100		-0.63
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1378124; hg19: chr8-98938388;