rs34764696
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_002821.5(PTK7):c.2330C>T(p.Ala777Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0643 in 1,614,106 control chromosomes in the GnomAD database, including 3,649 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_002821.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTK7 | NM_002821.5 | c.2330C>T | p.Ala777Val | missense_variant | 15/20 | ENST00000230419.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTK7 | ENST00000230419.9 | c.2330C>T | p.Ala777Val | missense_variant | 15/20 | 1 | NM_002821.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0539 AC: 8205AN: 152186Hom.: 238 Cov.: 33
GnomAD3 exomes AF: 0.0468 AC: 11762AN: 251360Hom.: 343 AF XY: 0.0486 AC XY: 6599AN XY: 135864
GnomAD4 exome AF: 0.0654 AC: 95608AN: 1461802Hom.: 3410 Cov.: 31 AF XY: 0.0647 AC XY: 47055AN XY: 727218
GnomAD4 genome ? AF: 0.0540 AC: 8223AN: 152304Hom.: 239 Cov.: 33 AF XY: 0.0520 AC XY: 3870AN XY: 74478
ClinVar
Submissions by phenotype
PTK7-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 02, 2020 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at