10-30026339-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_020848.4(JCAD):c.3809G>A(p.Arg1270Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000651 in 1,614,010 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign 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. R1270P) has been classified as Uncertain significance.
Frequency
Consequence
NM_020848.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
JCAD | NM_020848.4 | c.3809G>A | p.Arg1270Gln | missense_variant | 3/4 | ENST00000375377.2 | |
JCAD | NM_001350022.2 | c.3809G>A | p.Arg1270Gln | missense_variant | 4/5 | ||
JCAD | NM_001350001.2 | c.3395G>A | p.Arg1132Gln | missense_variant | 4/5 | ||
JCAD | NM_001350021.2 | c.3395G>A | p.Arg1132Gln | missense_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
JCAD | ENST00000375377.2 | c.3809G>A | p.Arg1270Gln | missense_variant | 3/4 | 5 | NM_020848.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152186Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000361 AC: 9AN: 249452Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135344
GnomAD4 exome AF: 0.0000670 AC: 98AN: 1461824Hom.: 0 Cov.: 30 AF XY: 0.0000715 AC XY: 52AN XY: 727226
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152186Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 08, 2022 | The c.3809G>A (p.R1270Q) alteration is located in exon 3 (coding exon 2) of the KIAA1462 gene. This alteration results from a G to A substitution at nucleotide position 3809, causing the arginine (R) at amino acid position 1270 to be replaced by a glutamine (Q). 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