rs906097776

Variant names:

• chr1-1632234-C-G
• rs906097776
• NM_006983.2:c.16C>G

Your query was ambiguous. Multiple possible variants found:

• chr1-1632234-C-G
• chr1-1632234-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_006983.2(MMP23B):​c.16C>G​(p.Arg6Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000059 in 1,186,088 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R6C) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 29)
  • Exomes 𝑓: 0.0000059 (0 hom.)
• Consequence: MMP23B NM_006983.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.187

Genes affected

MMP23B (HGNC:7171): (matrix metallopeptidase 23B) This gene (MMP23B) encodes a member of the matrix metalloproteinase (MMP) family, and it is part of a duplicated region of chromosome 1p36.3. Proteins of the matrix metalloproteinase (MMP) family are involved in the breakdown of extracellular matrix in normal physiological processes, such as embryonic development, reproduction, and tissue remodeling, as well as in disease processes, such as arthritis and metastasis. This gene belongs to the more telomeric copy of the duplicated region. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.045296073).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MMP23B	NM_006983.2	c.16C>G	p.Arg6Gly	missense_variant	Exon 1 of 8	ENST00000356026.10	NP_008914.1
MMP23B	XM_047432837.1	c.16C>G	p.Arg6Gly	missense_variant	Exon 1 of 8		XP_047288793.1
MMP23B	XM_047432838.1	c.16C>G	p.Arg6Gly	missense_variant	Exon 1 of 8		XP_047288794.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MMP23B	ENST00000356026.10	c.16C>G	p.Arg6Gly	missense_variant	Exon 1 of 8	1	NM_006983.2	ENSP00000348308.5
MMP23B	ENST00000378675.7	c.16C>G	p.Arg6Gly	missense_variant	Exon 1 of 7	1		ENSP00000367945.3
MMP23B	ENST00000472264.1	c.16C>G	p.Arg6Gly	missense_variant	Exon 1 of 3	3		ENSP00000424976.1
MMP23B	ENST00000512731.5	n.16C>G		non_coding_transcript_exon_variant	Exon 1 of 6	2		ENSP00000423780.1

Frequencies

GnomAD3 genomes Cov.: 29

GnomAD3 exomes AF: 0.000113 AC: 1 AN: 8838 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 5556

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000445

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000590 AC: 7 AN: 1186088 Hom.: 0 Cov.: 31 AF XY: 0.00000174 AC XY: 1 AN XY: 574426

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000229

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000609

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 29

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.050
BayesDel_addAF	Benign	-0.39	T
BayesDel_noAF	Benign	-0.47
CADD	Benign	8.3
DANN	Benign	0.65
DEOGEN2	Benign	0.077	T;.;.
Eigen	Benign	-1.3
Eigen_PC	Benign	-1.3
FATHMM_MKL	Benign	0.019	N
LIST_S2	Benign	0.34	T;T;T
M_CAP	Benign	0.062	D
MetaRNN	Benign	0.045	T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.0	N;.;.
PrimateAI	Uncertain	0.67	T
PROVEAN	Benign	-0.42	N;D;N
REVEL	Benign	0.043
Sift	Benign	0.59	T;D;D
Sift4G	Benign	0.33	T;D;T
Polyphen		0.0070	B;.;B
Vest4		0.099
MutPred		0.36		Loss of MoRF binding (P = 3e-04);Loss of MoRF binding (P = 3e-04);Loss of MoRF binding (P = 3e-04);
MVP		0.088
ClinPred		0.0093	T
GERP RS		-2.5
Varity_R		0.047
gMVP		0.27

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: rs906097776; hg19: chr1-1567613;