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GeneBe

17-55394523-A-G

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_012329.3(MMD):c.528T>C(p.Asp176=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0035 in 1,512,682 control chromosomes in the GnomAD database, including 192 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.018 ( 115 hom., cov: 33)
Exomes 𝑓: 0.0018 ( 77 hom. )

Consequence

MMD
NM_012329.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.862
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.68).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 17-55394523-A-G is Benign according to our data. Variant chr17-55394523-A-G is described in ClinVar as [Benign]. Clinvar id is 778717.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-0.862 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0627 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MMDNM_012329.3 linkuse as main transcriptc.528T>C p.Asp176= synonymous_variant 7/7 ENST00000262065.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MMDENST00000262065.8 linkuse as main transcriptc.528T>C p.Asp176= synonymous_variant 7/71 NM_012329.3 P1
MMDENST00000649377.1 linkuse as main transcriptc.621T>C p.Asp207= synonymous_variant 8/8

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0183
AC:
2789
AN:
152168
Hom.:
114
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0648
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00478
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.000132
Gnomad OTH
AF:
0.0101
GnomAD3 exomes
AF:
0.00498
AC:
845
AN:
169670
Hom.:
32
AF XY:
0.00336
AC XY:
313
AN XY:
93196
show subpopulations
Gnomad AFR exome
AF:
0.0656
Gnomad AMR exome
AF:
0.00299
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000115
Gnomad FIN exome
AF:
0.0000518
Gnomad NFE exome
AF:
0.000222
Gnomad OTH exome
AF:
0.00256
GnomAD4 exome
AF:
0.00183
AC:
2496
AN:
1360396
Hom.:
77
Cov.:
30
AF XY:
0.00161
AC XY:
1087
AN XY:
674582
show subpopulations
Gnomad4 AFR exome
AF:
0.0679
Gnomad4 AMR exome
AF:
0.00307
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000143
Gnomad4 FIN exome
AF:
0.0000195
Gnomad4 NFE exome
AF:
0.000210
Gnomad4 OTH exome
AF:
0.00489
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0183
AC:
2793
AN:
152286
Hom.:
115
Cov.:
33
AF XY:
0.0169
AC XY:
1261
AN XY:
74460
show subpopulations
Gnomad4 AFR
AF:
0.0647
Gnomad4 AMR
AF:
0.00477
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000132
Gnomad4 OTH
AF:
0.00995
Alfa
AF:
0.0117
Hom.:
25
Bravo
AF:
0.0216
Asia WGS
AF:
0.00375
AC:
13
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeAug 21, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.68
Cadd
Benign
0.86
Dann
Benign
0.60
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2229672; hg19: chr17-53471884; API