NM_012329.3:c.23A>G

Variant names:

• chr17-55421673-T-C
• NM_012329.3:c.23A>G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_012329.3(MMD):​c.23A>G​(p.Gln8Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000692 in 1,445,854 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
• Consequence: MMD NM_012329.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 1.51

Genes affected

MMD (HGNC:7153): (monocyte to macrophage differentiation associated) This protein is expressed by in vitro differentiated macrophages but not freshly isolated monocytes. Although sequence analysis identifies seven potential transmembrane domains, this protein has little homology to G-protein receptors and it has not been positively identified as a receptor. A suggested alternative function is that of an ion channel protein in maturing macrophages. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.11390725).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MMD	NM_012329.3	c.23A>G	p.Gln8Arg	missense_variant	Exon 1 of 7	ENST00000262065.8	NP_036461.2
MMD	XM_047435708.1	c.23A>G	p.Gln8Arg	missense_variant	Exon 1 of 5		XP_047291664.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MMD	ENST00000262065.8	c.23A>G	p.Gln8Arg	missense_variant	Exon 1 of 7	1	NM_012329.3	ENSP00000262065.3
MMD	ENST00000649377.1	c.23A>G	p.Gln8Arg	missense_variant	Exon 1 of 8			ENSP00000497849.1
MMD	ENST00000571578.1	c.23A>G	p.Gln8Arg	missense_variant	Exon 1 of 5	3		ENSP00000459202.1
MMD	ENST00000577038.1	n.125A>G		non_coding_transcript_exon_variant	Exon 1 of 2	2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 6.92e-7 AC: 1 AN: 1445854 Hom.: 0 Cov.: 33 AF XY: 0.00000139 AC XY: 1 AN XY: 719462

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000237

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Oct 17, 2024

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.23A>G (p.Q8R) alteration is located in exon 1 (coding exon 1) of the MMD gene. This alteration results from a A to G substitution at nucleotide position 23, causing the glutamine (Q) at amino acid position 8 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.10
BayesDel_addAF	Benign	-0.064	T
BayesDel_noAF	Benign	-0.33
CADD	Benign	21
DANN	Benign	0.94
DEOGEN2	Benign	0.21	T;.;.
Eigen	Benign	-0.25
Eigen_PC	Benign	-0.050
FATHMM_MKL	Uncertain	0.87	D
LIST_S2	Benign	0.59	T;T;T
M_CAP	Benign	0.019	T
MetaRNN	Benign	0.11	T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	1.2	L;.;.
PrimateAI	Uncertain	0.71	T
PROVEAN	Benign	-0.44	N;.;.
REVEL	Benign	0.098
Sift	Benign	0.69	T;.;.
Sift4G	Benign	0.39	T;.;T
Polyphen		0.0	B;.;.
Vest4		0.23
MutPred		0.28		Gain of methylation at Q8 (P = 0.0076);Gain of methylation at Q8 (P = 0.0076);Gain of methylation at Q8 (P = 0.0076);
MVP		0.40
MPC		0.71
ClinPred		0.29	T
GERP RS		4.6
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.22
gMVP		0.32

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr17-53499034;