chr19-47476679-C-T
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_007059.4(KPTN):c.1035G>A(p.Ser345=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000709 in 1,612,636 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. S345S) has been classified as Likely benign.
Frequency
Consequence
NM_007059.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KPTN | NM_007059.4 | c.1035G>A | p.Ser345= | synonymous_variant | 11/12 | ENST00000338134.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KPTN | ENST00000338134.8 | c.1035G>A | p.Ser345= | synonymous_variant | 11/12 | 1 | NM_007059.4 | P1 | |
ENST00000669287.1 | n.286C>T | non_coding_transcript_exon_variant | 2/2 | ||||||
KPTN | ENST00000594208.5 | c.*669G>A | 3_prime_UTR_variant, NMD_transcript_variant | 12/13 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000468 AC: 71AN: 151622Hom.: 0 Cov.: 27
GnomAD3 exomes AF: 0.000522 AC: 128AN: 245090Hom.: 0 AF XY: 0.000509 AC XY: 68AN XY: 133468
GnomAD4 exome AF: 0.000734 AC: 1073AN: 1460896Hom.: 2 Cov.: 31 AF XY: 0.000736 AC XY: 535AN XY: 726642
GnomAD4 genome AF: 0.000468 AC: 71AN: 151740Hom.: 0 Cov.: 27 AF XY: 0.000445 AC XY: 33AN XY: 74116
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Dec 09, 2016 | - - |
Macrocephaly-developmental delay syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 16, 2023 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2024 | KPTN: BP4, BP7 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at