7-75988086-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_031925.3(TMEM120A):c.626C>T(p.Thr209Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000429 in 1,607,344 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000053 ( 0 hom., cov: 30)
Exomes 𝑓: 0.000042 ( 0 hom. )
Consequence
TMEM120A
NM_031925.3 missense
NM_031925.3 missense
Scores
2
7
2
Clinical Significance
Conservation
PhyloP100: 5.83
Genes affected
TMEM120A (HGNC:21697): (transmembrane protein 120A) Predicted to enable ion channel activity. Involved in fat cell differentiation; protein heterooligomerization; and protein homooligomerization. Predicted to be located in plasma membrane. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM120A | NM_031925.3 | c.626C>T | p.Thr209Met | missense_variant | 7/12 | ENST00000493111.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM120A | ENST00000493111.7 | c.626C>T | p.Thr209Met | missense_variant | 7/12 | 1 | NM_031925.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152216Hom.: 0 Cov.: 30
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GnomAD3 exomes AF: 0.0000377 AC: 9AN: 238550Hom.: 0 AF XY: 0.0000231 AC XY: 3AN XY: 129958
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GnomAD4 exome AF: 0.0000419 AC: 61AN: 1455128Hom.: 0 Cov.: 38 AF XY: 0.0000401 AC XY: 29AN XY: 723328
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GnomAD4 genome ? AF: 0.0000526 AC: 8AN: 152216Hom.: 0 Cov.: 30 AF XY: 0.0000403 AC XY: 3AN XY: 74368
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 05, 2023 | The c.626C>T (p.T209M) alteration is located in exon 7 (coding exon 7) of the TMEM120A gene. This alteration results from a C to T substitution at nucleotide position 626, causing the threonine (T) at amino acid position 209 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Uncertain
Cadd
Pathogenic
Dann
Benign
DEOGEN2
Benign
T;.;.
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D
MetaRNN
Uncertain
T;T;T
MutationAssessor
Pathogenic
M;.;.
PrimateAI
Uncertain
T
Sift4G
Uncertain
D;D;D
Polyphen
D;.;.
Vest4
MVP
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
Name
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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