chr10-114204884-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001395205.1(TDRD1):c.1288C>A(p.Pro430Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000758 in 1,582,424 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001395205.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TDRD1 | NM_001395205.1 | c.1288C>A | p.Pro430Thr | missense_variant | 10/25 | ENST00000695399.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TDRD1 | ENST00000695399.1 | c.1288C>A | p.Pro430Thr | missense_variant | 10/25 | NM_001395205.1 | P4 | ||
TDRD1 | ENST00000251864.7 | c.1288C>A | p.Pro430Thr | missense_variant | 10/26 | 1 | A2 | ||
TDRD1 | ENST00000369282.5 | c.1288C>A | p.Pro430Thr | missense_variant | 10/25 | 5 | A2 | ||
TDRD1 | ENST00000369280.1 | c.1288C>A | p.Pro430Thr | missense_variant | 10/24 | 5 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152074Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000444 AC: 10AN: 225078Hom.: 0 AF XY: 0.0000410 AC XY: 5AN XY: 121896
GnomAD4 exome AF: 0.00000699 AC: 10AN: 1430350Hom.: 0 Cov.: 30 AF XY: 0.00000705 AC XY: 5AN XY: 709500
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152074Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74280
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 31, 2023 | The c.1288C>A (p.P430T) alteration is located in exon 10 (coding exon 9) of the TDRD1 gene. This alteration results from a C to A substitution at nucleotide position 1288, causing the proline (P) at amino acid position 430 to be replaced by a threonine (T). 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