3-33093568-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001039770.3(TMPPE):c.628G>A(p.Val210Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000898 in 1,614,156 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V210L) has been classified as Uncertain significance.
Frequency
Consequence
NM_001039770.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMPPE | NM_001039770.3 | c.628G>A | p.Val210Met | missense_variant | 2/2 | ENST00000342462.5 | |
GLB1 | NM_000404.4 | c.75+3443G>A | intron_variant | ENST00000307363.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMPPE | ENST00000342462.5 | c.628G>A | p.Val210Met | missense_variant | 2/2 | 2 | NM_001039770.3 | P1 | |
GLB1 | ENST00000307363.10 | c.75+3443G>A | intron_variant | 1 | NM_000404.4 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152186Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000163 AC: 41AN: 251164Hom.: 0 AF XY: 0.000221 AC XY: 30AN XY: 135740
GnomAD4 exome AF: 0.0000944 AC: 138AN: 1461852Hom.: 2 Cov.: 32 AF XY: 0.000150 AC XY: 109AN XY: 727218
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152304Hom.: 0 Cov.: 33 AF XY: 0.0000671 AC XY: 5AN XY: 74472
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 29, 2022 | The c.628G>A (p.V210M) alteration is located in exon 2 (coding exon 1) of the TMPPE gene. This alteration results from a G to A substitution at nucleotide position 628, causing the valine (V) at amino acid position 210 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at