2-96605442-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001115016.3(KANSL3):āc.1811A>Gā(p.His604Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,656 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001115016.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KANSL3 | NM_001115016.3 | c.1811A>G | p.His604Arg | missense_variant | 15/21 | ENST00000431828.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KANSL3 | ENST00000431828.6 | c.1811A>G | p.His604Arg | missense_variant | 15/21 | 1 | NM_001115016.3 | P3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 249238Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135214
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461656Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727122
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 28, 2023 | The c.1811A>G (p.H604R) alteration is located in exon 15 (coding exon 14) of the KANSL3 gene. This alteration results from a A to G substitution at nucleotide position 1811, causing the histidine (H) at amino acid position 604 to be replaced by an arginine (R). 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