chr9-97431021-G-A
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBS1_Supporting
The NM_014290.3(TDRD7):c.296G>A(p.Arg99His) variant causes a missense change. The variant allele was found at a frequency of 0.0000316 in 1,613,914 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. R99C) has been classified as Uncertain significance.
Frequency
Consequence
NM_014290.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TDRD7 | NM_014290.3 | c.296G>A | p.Arg99His | missense_variant | 3/17 | ENST00000355295.5 | |
TDRD7 | NM_001302884.2 | c.74G>A | p.Arg25His | missense_variant | 2/16 | ||
TDRD7 | XM_047423111.1 | c.296G>A | p.Arg99His | missense_variant | 3/17 | ||
TDRD7 | XM_047423113.1 | c.296G>A | p.Arg99His | missense_variant | 3/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TDRD7 | ENST00000355295.5 | c.296G>A | p.Arg99His | missense_variant | 3/17 | 1 | NM_014290.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152182Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251108Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135694
GnomAD4 exome AF: 0.0000328 AC: 48AN: 1461614Hom.: 0 Cov.: 32 AF XY: 0.0000303 AC XY: 22AN XY: 727112
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152300Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74482
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Mar 31, 2022 | In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at