14-20429511-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001365790.2(KLHL33):c.1832A>C(p.Asn611Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 1,552,108 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. N611S) has been classified as Uncertain significance.
Frequency
Consequence
NM_001365790.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KLHL33 | NM_001365790.2 | c.1832A>C | p.Asn611Thr | missense_variant | 4/5 | ENST00000636854.3 | |
KLHL33 | NM_001109997.3 | c.1040A>C | p.Asn347Thr | missense_variant | 3/4 | ||
KLHL33 | XM_011536450.3 | c.1832A>C | p.Asn611Thr | missense_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KLHL33 | ENST00000636854.3 | c.1832A>C | p.Asn611Thr | missense_variant | 4/5 | 5 | NM_001365790.2 | P1 | |
KLHL33 | ENST00000637228.1 | c.1832A>C | p.Asn611Thr | missense_variant | 3/4 | 5 | |||
KLHL33 | ENST00000344581.4 | c.1040A>C | p.Asn347Thr | missense_variant | 3/4 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152100Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000252 AC: 4AN: 158596Hom.: 0 AF XY: 0.0000359 AC XY: 3AN XY: 83492
GnomAD4 exome AF: 0.0000186 AC: 26AN: 1400008Hom.: 0 Cov.: 37 AF XY: 0.0000232 AC XY: 16AN XY: 690472
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152100Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74302
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 22, 2023 | The c.1040A>C (p.N347T) alteration is located in exon 3 (coding exon 2) of the KLHL33 gene. This alteration results from a A to C substitution at nucleotide position 1040, causing the asparagine (N) at amino acid position 347 to be replaced by a threonine (T). 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