chr19-45347465-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_177417.3(KLC3):c.508C>T(p.Arg170Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000459 in 1,612,392 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_177417.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KLC3 | NM_177417.3 | c.508C>T | p.Arg170Cys | missense_variant | 4/13 | ENST00000391946.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KLC3 | ENST00000391946.7 | c.508C>T | p.Arg170Cys | missense_variant | 4/13 | 1 | NM_177417.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152072Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000323 AC: 8AN: 247712Hom.: 0 AF XY: 0.0000372 AC XY: 5AN XY: 134500
GnomAD4 exome AF: 0.0000486 AC: 71AN: 1460320Hom.: 0 Cov.: 32 AF XY: 0.0000482 AC XY: 35AN XY: 726482
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152072Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74274
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 07, 2023 | The c.508C>T (p.R170C) alteration is located in exon 4 (coding exon 3) of the KLC3 gene. This alteration results from a C to T substitution at nucleotide position 508, causing the arginine (R) at amino acid position 170 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at