chr19-51014940-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_145888.3(KLK10):c.691G>A(p.Gly231Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,613,446 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G231D) has been classified as Uncertain significance.
Frequency
Consequence
NM_145888.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KLK10 | NM_145888.3 | c.691G>A | p.Gly231Ser | missense_variant | 6/6 | ENST00000358789.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KLK10 | ENST00000358789.8 | c.691G>A | p.Gly231Ser | missense_variant | 6/6 | 1 | NM_145888.3 | P1 | |
KLK10 | ENST00000309958.7 | c.691G>A | p.Gly231Ser | missense_variant | 6/6 | 1 | P1 | ||
KLK10 | ENST00000601467.1 | c.*267G>A | 3_prime_UTR_variant, NMD_transcript_variant | 5/5 | 1 | ||||
KLK10 | ENST00000391805.5 | c.691G>A | p.Gly231Ser | missense_variant | 6/6 | 5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152118Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000798 AC: 2AN: 250750Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135524
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461328Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 726986
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152118Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74306
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 25, 2023 | The c.691G>A (p.G231S) alteration is located in exon 6 (coding exon 5) of the KLK10 gene. This alteration results from a G to A substitution at nucleotide position 691, causing the glycine (G) at amino acid position 231 to be replaced by a serine (S). 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