chr2-24790533-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001013663.2(PTRHD1):āc.301A>Gā(p.Lys101Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000607 in 1,614,196 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ā ).
Frequency
Consequence
NM_001013663.2 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 |
---|---|---|---|---|---|---|---|
PTRHD1 | NM_001013663.2 | c.301A>G | p.Lys101Glu | missense_variant | 2/2 | ENST00000328379.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTRHD1 | ENST00000328379.6 | c.301A>G | p.Lys101Glu | missense_variant | 2/2 | 1 | NM_001013663.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000283 AC: 43AN: 152212Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000266 AC: 67AN: 251448Hom.: 0 AF XY: 0.000265 AC XY: 36AN XY: 135896
GnomAD4 exome AF: 0.000641 AC: 937AN: 1461866Hom.: 0 Cov.: 30 AF XY: 0.000648 AC XY: 471AN XY: 727238
GnomAD4 genome AF: 0.000282 AC: 43AN: 152330Hom.: 0 Cov.: 32 AF XY: 0.000228 AC XY: 17AN XY: 74490
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 13, 2022 | The c.301A>G (p.K101E) alteration is located in exon 2 (coding exon 2) of the PTRHD1 gene. This alteration results from a A to G substitution at nucleotide position 301, causing the lysine (K) at amino acid position 101 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Apr 27, 2023 | BP4 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at