6-18166306-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001364614.2(KDM1B):āc.345A>Cā(p.Lys115Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000211 in 1,612,130 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001364614.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KDM1B | NM_001364614.2 | c.345A>C | p.Lys115Asn | missense_variant | 6/22 | ENST00000650836.2 | NP_001351543.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KDM1B | ENST00000650836.2 | c.345A>C | p.Lys115Asn | missense_variant | 6/22 | NM_001364614.2 | ENSP00000499208.1 | |||
KDM1B | ENST00000546309.6 | c.-19+10893A>C | intron_variant | 1 | ENSP00000442670.1 | |||||
KDM1B | ENST00000449850.2 | c.345A>C | p.Lys115Asn | missense_variant | 6/22 | 5 | ENSP00000405669.2 | |||
KDM1B | ENST00000297792.9 | c.345A>C | p.Lys115Asn | missense_variant | 6/18 | 2 | ENSP00000297792.5 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152210Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251438Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135894
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1459802Hom.: 0 Cov.: 28 AF XY: 0.0000179 AC XY: 13AN XY: 726412
GnomAD4 genome AF: 0.0000656 AC: 10AN: 152328Hom.: 0 Cov.: 32 AF XY: 0.0000805 AC XY: 6AN XY: 74492
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 24, 2022 | The c.345A>C (p.K115N) alteration is located in exon 6 (coding exon 4) of the KDM1B gene. This alteration results from a A to C substitution at nucleotide position 345, causing the lysine (K) at amino acid position 115 to be replaced by an asparagine (N). 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