chr12-72563025-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_013381.3(TRHDE):c.2027A>G(p.Lys676Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000254 in 1,595,776 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_013381.3 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 |
---|---|---|---|---|---|---|---|
TRHDE | NM_013381.3 | c.2027A>G | p.Lys676Arg | missense_variant | 9/19 | ENST00000261180.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRHDE | ENST00000261180.10 | c.2027A>G | p.Lys676Arg | missense_variant | 9/19 | 1 | NM_013381.3 | P1 | |
TRHDE | ENST00000549138.5 | n.456A>G | non_coding_transcript_exon_variant | 3/7 | 5 | ||||
TRHDE | ENST00000549401.5 | n.174A>G | non_coding_transcript_exon_variant | 1/5 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000191 AC: 29AN: 152164Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000172 AC: 41AN: 238992Hom.: 0 AF XY: 0.000162 AC XY: 21AN XY: 129428
GnomAD4 exome AF: 0.000260 AC: 376AN: 1443612Hom.: 0 Cov.: 28 AF XY: 0.000264 AC XY: 190AN XY: 718576
GnomAD4 genome ? AF: 0.000191 AC: 29AN: 152164Hom.: 0 Cov.: 33 AF XY: 0.000135 AC XY: 10AN XY: 74322
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 06, 2021 | The c.1892A>G (p.K631R) alteration is located in exon 9 (coding exon 9) of the TRHDE gene. This alteration results from a A to G substitution at nucleotide position 1892, causing the lysine (K) at amino acid position 631 to be replaced by an arginine (R). 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