chr1-175379587-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003285.3(TNR):c.1928G>A(p.Arg643Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.66 in 1,613,402 control chromosomes in the GnomAD database, including 353,095 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_003285.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNR | NM_003285.3 | c.1928G>A | p.Arg643Lys | missense_variant | 9/23 | ENST00000367674.7 | |
TNR | NM_001328635.2 | c.929G>A | p.Arg310Lys | missense_variant | 9/23 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNR | ENST00000367674.7 | c.1928G>A | p.Arg643Lys | missense_variant | 9/23 | 5 | NM_003285.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.663 AC: 100683AN: 151850Hom.: 33526 Cov.: 31
GnomAD3 exomes AF: 0.675 AC: 169575AN: 251122Hom.: 57773 AF XY: 0.671 AC XY: 90994AN XY: 135698
GnomAD4 exome AF: 0.660 AC: 964568AN: 1461432Hom.: 319539 Cov.: 53 AF XY: 0.660 AC XY: 479634AN XY: 726998
GnomAD4 genome ? AF: 0.663 AC: 100767AN: 151970Hom.: 33556 Cov.: 31 AF XY: 0.662 AC XY: 49188AN XY: 74270
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at