chr19-47475493-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_007059.4(KPTN):c.1234G>A(p.Val412Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,218 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (★).
Frequency
Consequence
NM_007059.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KPTN | NM_007059.4 | c.1234G>A | p.Val412Met | missense_variant | 12/12 | ENST00000338134.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KPTN | ENST00000338134.8 | c.1234G>A | p.Val412Met | missense_variant | 12/12 | 1 | NM_007059.4 | P1 | |
ENST00000669287.1 | n.69-969C>T | intron_variant, non_coding_transcript_variant | |||||||
KPTN | ENST00000600551.1 | n.125G>A | non_coding_transcript_exon_variant | 2/2 | 5 | ||||
KPTN | ENST00000594208.5 | c.*868G>A | 3_prime_UTR_variant, NMD_transcript_variant | 13/13 | 2 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461218Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 726872
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
Macrocephaly-developmental delay syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Baylor Genetics | Feb 08, 2020 | This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868]. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at