6-130441012-A-T
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001258277.2(TMEM200A):c.590A>T(p.Asn197Ile) variant causes a missense change. The variant allele was found at a frequency of 0.00000342 in 1,461,688 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000034 ( 0 hom. )
Consequence
TMEM200A
NM_001258277.2 missense
NM_001258277.2 missense
Scores
2
17
Clinical Significance
Conservation
PhyloP100: 4.66
Genes affected
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ACMG classification
Classification made for transcript
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=0.07542375).
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TMEM200A | ENST00000296978.4 | c.590A>T | p.Asn197Ile | missense_variant | 3/3 | 1 | NM_001258277.2 | ENSP00000296978.3 | ||
TMEM200A | ENST00000392429.1 | c.590A>T | p.Asn197Ile | missense_variant | 2/2 | 1 | ENSP00000376224.1 | |||
TMEM200A | ENST00000545622.5 | c.590A>T | p.Asn197Ile | missense_variant | 2/2 | 2 | ENSP00000438928.1 | |||
TMEM200A | ENST00000617887.4 | c.590A>T | p.Asn197Ile | missense_variant | 2/2 | 2 | ENSP00000480294.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 250758Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135500
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GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461688Hom.: 0 Cov.: 33 AF XY: 0.00000413 AC XY: 3AN XY: 727140
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GnomAD4 genome Cov.: 32
GnomAD4 genome
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32
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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 | Dec 10, 2024 | The c.590A>T (p.N197I) alteration is located in exon 2 (coding exon 1) of the TMEM200A gene. This alteration results from a A to T substitution at nucleotide position 590, causing the asparagine (N) at amino acid position 197 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;T;T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
.;.;T;.
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;N;N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;.;N;N
REVEL
Benign
Sift
Benign
T;.;T;T
Sift4G
Benign
T;T;T;T
Polyphen
B;B;B;B
Vest4
MutPred
Loss of loop (P = 0.0203);Loss of loop (P = 0.0203);Loss of loop (P = 0.0203);Loss of loop (P = 0.0203);
MVP
MPC
0.19
ClinPred
T
GERP RS
Varity_R
gMVP
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