chr19-47475414-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_007059.4(KPTN):c.*2C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 1,611,002 control chromosomes in the GnomAD database, including 14,306 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.14 ( 1707 hom., cov: 31)
Exomes 𝑓: 0.12 ( 12599 hom. )
Consequence
KPTN
NM_007059.4 3_prime_UTR
NM_007059.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.521
Genes affected
KPTN (HGNC:6404): (kaptin, actin binding protein) This gene encodes a filamentous-actin-associated protein, which is involved in actin dynamics and plays an important role in neuromorphogenesis. This protein is part of the KICSTOR protein complex that localizes to lysosomes. Mutations in this gene result in an autosomal recessive form of intellectual disability. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
?
Variant 19-47475414-G-A is Benign according to our data. Variant chr19-47475414-G-A is described in ClinVar as [Benign]. Clinvar id is 1179592.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KPTN | NM_007059.4 | c.*2C>T | 3_prime_UTR_variant | 12/12 | ENST00000338134.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KPTN | ENST00000338134.8 | c.*2C>T | 3_prime_UTR_variant | 12/12 | 1 | NM_007059.4 | P1 | ||
ENST00000669287.1 | n.69-1048G>A | intron_variant, non_coding_transcript_variant | |||||||
KPTN | ENST00000600551.1 | n.204C>T | non_coding_transcript_exon_variant | 2/2 | 5 | ||||
KPTN | ENST00000594208.5 | c.*947C>T | 3_prime_UTR_variant, NMD_transcript_variant | 13/13 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.145 AC: 22005AN: 151992Hom.: 1702 Cov.: 31
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GnomAD3 exomes AF: 0.150 AC: 36889AN: 246172Hom.: 3256 AF XY: 0.144 AC XY: 19286AN XY: 133776
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GnomAD4 exome AF: 0.124 AC: 181377AN: 1458892Hom.: 12599 Cov.: 31 AF XY: 0.124 AC XY: 90006AN XY: 725670
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GnomAD4 genome ? AF: 0.145 AC: 22055AN: 152110Hom.: 1707 Cov.: 31 AF XY: 0.149 AC XY: 11047AN XY: 74360
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 04, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at