chr10-114204830-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001395205.1(TDRD1):c.1234A>G(p.Ile412Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000613 in 1,599,030 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 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
Genome browser will be placed here
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.1234A>G | p.Ile412Val | missense_variant | 10/25 | ENST00000695399.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TDRD1 | ENST00000695399.1 | c.1234A>G | p.Ile412Val | missense_variant | 10/25 | NM_001395205.1 | P4 | ||
TDRD1 | ENST00000251864.7 | c.1234A>G | p.Ile412Val | missense_variant | 10/26 | 1 | A2 | ||
TDRD1 | ENST00000369282.5 | c.1234A>G | p.Ile412Val | missense_variant | 10/25 | 5 | A2 | ||
TDRD1 | ENST00000369280.1 | c.1234A>G | p.Ile412Val | missense_variant | 10/24 | 5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152168Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000114 AC: 27AN: 237568Hom.: 0 AF XY: 0.000125 AC XY: 16AN XY: 128338
GnomAD4 exome AF: 0.0000629 AC: 91AN: 1446862Hom.: 1 Cov.: 30 AF XY: 0.0000626 AC XY: 45AN XY: 718598
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152168Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74338
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 21, 2022 | The c.1234A>G (p.I412V) alteration is located in exon 10 (coding exon 9) of the TDRD1 gene. This alteration results from a A to G substitution at nucleotide position 1234, causing the isoleucine (I) at amino acid position 412 to be replaced by a valine (V). 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