7-75988501-G-T
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_031925.3(TMEM120A):c.393C>A(p.Asp131Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000685 in 1,459,714 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 28)
Exomes 𝑓: 0.0000069 ( 0 hom. )
Consequence
TMEM120A
NM_031925.3 missense
NM_031925.3 missense
Scores
2
4
5
Clinical Significance
Conservation
PhyloP100: 0.283
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
Ensembl
Frequencies
GnomAD3 genomes Cov.: 28
GnomAD3 genomes
Cov.:
28
GnomAD3 exomes AF: 0.00000806 AC: 2AN: 248120Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135124
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GnomAD4 exome AF: 0.00000685 AC: 10AN: 1459714Hom.: 0 Cov.: 34 AF XY: 0.00000689 AC XY: 5AN XY: 726138
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GnomAD4 genome Cov.: 28
GnomAD4 genome
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28
ExAC
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2
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 | Nov 14, 2023 | The c.393C>A (p.D131E) alteration is located in exon 5 (coding exon 5) of the TMEM120A gene. This alteration results from a C to A substitution at nucleotide position 393, causing the aspartic acid (D) at amino acid position 131 to be replaced by a glutamic acid (E). 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
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T;T;.;.;.
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;.;D;D;D
MetaRNN
Uncertain
T;T;T;T;T
MutationAssessor
Uncertain
M;.;.;.;.
PrimateAI
Pathogenic
D
Sift4G
Benign
T;T;T;T;T
Polyphen
P;.;.;.;.
Vest4
MVP
GERP RS
Varity_R
gMVP
Splicing
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Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at