19-2790612-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003249.5(THOP1):c.208G>A(p.Asp70Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000369 in 1,573,190 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003249.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
THOP1 | ENST00000307741.11 | c.208G>A | p.Asp70Asn | missense_variant | 2/13 | 1 | NM_003249.5 | ENSP00000304467.5 | ||
THOP1 | ENST00000585338.1 | c.178G>A | p.Asp60Asn | missense_variant | 3/6 | 3 | ENSP00000465545.1 | |||
THOP1 | ENST00000585673.5 | n.357G>A | non_coding_transcript_exon_variant | 2/6 | 3 | |||||
THOP1 | ENST00000586780.1 | n.304G>A | non_coding_transcript_exon_variant | 2/3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152218Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000337 AC: 7AN: 207998Hom.: 0 AF XY: 0.0000179 AC XY: 2AN XY: 111560
GnomAD4 exome AF: 0.0000373 AC: 53AN: 1420972Hom.: 0 Cov.: 31 AF XY: 0.0000327 AC XY: 23AN XY: 704354
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152218Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 25, 2022 | The c.208G>A (p.D70N) alteration is located in exon 2 (coding exon 2) of the THOP1 gene. This alteration results from a G to A substitution at nucleotide position 208, causing the aspartic acid (D) at amino acid position 70 to be replaced by an asparagine (N). 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