8-27422364-C-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The ENST00000346049.10(PTK2B):c.532C>T(p.Leu178=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000915 in 1,613,210 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. L178L) has been classified as Benign.
Frequency
Consequence
ENST00000346049.10 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PTK2B | NM_173176.3 | c.532C>T | p.Leu178= | synonymous_variant | 5/31 | ENST00000346049.10 | NP_775268.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PTK2B | ENST00000346049.10 | c.532C>T | p.Leu178= | synonymous_variant | 5/31 | 1 | NM_173176.3 | ENSP00000332816 | A1 |
Frequencies
GnomAD3 genomes AF: 0.00366 AC: 557AN: 152266Hom.: 3 Cov.: 33
GnomAD3 exomes AF: 0.00133 AC: 330AN: 248618Hom.: 1 AF XY: 0.00126 AC XY: 169AN XY: 134454
GnomAD4 exome AF: 0.000616 AC: 900AN: 1460826Hom.: 6 Cov.: 30 AF XY: 0.000614 AC XY: 446AN XY: 726716
GnomAD4 genome AF: 0.00378 AC: 576AN: 152384Hom.: 5 Cov.: 33 AF XY: 0.00380 AC XY: 283AN XY: 74520
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jun 18, 2018 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at