8-97926160-C-T

Position:

• chr8-97926160-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
MATN2	NM_002380.5	c.143-4793C>T		intron_variant		ENST00000254898.7	NP_002371.3
MATN2	NM_001317748.2	c.143-4793C>T		intron_variant			NP_001304677.1
MATN2	NM_030583.4	c.143-4793C>T		intron_variant			NP_085072.2
MATN2	XM_005250920.3	c.143-4793C>T		intron_variant			XP_005250977.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MATN2	ENST00000254898.7	c.143-4793C>T		intron_variant		1	NM_002380.5	ENSP00000254898	P4

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

Gnomad4 AFR AF: 0.544

Gnomad4 AMR AF: 0.743

Gnomad4 ASJ AF: 0.699

Gnomad4 EAS AF: 0.922

Gnomad4 SAS AF: 0.821

Gnomad4 FIN AF: 0.623

Gnomad4 NFE AF: 0.675

Gnomad4 OTH AF: 0.658

Alfa AF: 0.674 Hom.: 58143

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

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

LitVar

Other links and lift over

dbSNP: rs1378124; hg19: chr8-98938388;