rs4476230
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_012329.3(MMD):c.*590A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 152,522 control chromosomes in the GnomAD database, including 8,682 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 0.30 ( 8653 hom., cov: 33)
Exomes 𝑓: 0.36 ( 29 hom. )
Consequence
MMD
NM_012329.3 3_prime_UTR
NM_012329.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.437
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MMD | NM_012329.3 | c.*590A>C | 3_prime_UTR_variant | 7/7 | ENST00000262065.8 | NP_036461.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MMD | ENST00000262065.8 | c.*590A>C | 3_prime_UTR_variant | 7/7 | 1 | NM_012329.3 | ENSP00000262065 | P1 | ||
MMD | ENST00000649377.1 | c.*590A>C | 3_prime_UTR_variant | 8/8 | ENSP00000497849 |
Frequencies
GnomAD3 genomes AF: 0.304 AC: 46220AN: 151976Hom.: 8635 Cov.: 33
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GnomAD4 exome AF: 0.357 AC: 153AN: 428Hom.: 29 Cov.: 0 AF XY: 0.337 AC XY: 87AN XY: 258
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GnomAD4 genome AF: 0.304 AC: 46259AN: 152094Hom.: 8653 Cov.: 33 AF XY: 0.300 AC XY: 22334AN XY: 74338
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at