chr8-27430997-C-A
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_173176.3(PTK2B):c.791C>A(p.Thr264Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0042 in 1,614,046 control chromosomes in the GnomAD database, including 21 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 Likely benign (★★).
Frequency
Consequence
NM_173176.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTK2B | NM_173176.3 | c.791C>A | p.Thr264Asn | missense_variant | 8/31 | ENST00000346049.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTK2B | ENST00000346049.10 | c.791C>A | p.Thr264Asn | missense_variant | 8/31 | 1 | NM_173176.3 | A1 |
Frequencies
GnomAD3 genomes AF: 0.00348 AC: 529AN: 152222Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00290 AC: 729AN: 251238Hom.: 5 AF XY: 0.00288 AC XY: 391AN XY: 135776
GnomAD4 exome AF: 0.00428 AC: 6252AN: 1461706Hom.: 20 Cov.: 32 AF XY: 0.00418 AC XY: 3036AN XY: 727156
GnomAD4 genome AF: 0.00347 AC: 529AN: 152340Hom.: 1 Cov.: 33 AF XY: 0.00318 AC XY: 237AN XY: 74492
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 08, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at