chr16-20739050-G-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBS1_SupportingBS2
The NM_017736.5(THUMPD1):c.253C>T(p.Pro85Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000655 in 1,614,126 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_017736.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
THUMPD1 | NM_017736.5 | c.253C>T | p.Pro85Ser | missense_variant | 2/4 | ENST00000396083.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
THUMPD1 | ENST00000396083.7 | c.253C>T | p.Pro85Ser | missense_variant | 2/4 | 1 | NM_017736.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000447 AC: 68AN: 152138Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000497 AC: 125AN: 251414Hom.: 2 AF XY: 0.000589 AC XY: 80AN XY: 135868
GnomAD4 exome AF: 0.000677 AC: 989AN: 1461870Hom.: 3 Cov.: 32 AF XY: 0.000688 AC XY: 500AN XY: 727238
GnomAD4 genome AF: 0.000447 AC: 68AN: 152256Hom.: 0 Cov.: 32 AF XY: 0.000403 AC XY: 30AN XY: 74436
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 22, 2021 | The c.253C>T (p.P85S) alteration is located in exon 2 (coding exon 2) of the THUMPD1 gene. This alteration results from a C to T substitution at nucleotide position 253, causing the proline (P) at amino acid position 85 to be replaced by a serine (S). 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