chr10-30026339-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_020848.4(JCAD):c.3809G>C(p.Arg1270Pro) variant causes a missense change. The variant allele was found at a frequency of 0.00000342 in 1,461,824 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. R1270Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_020848.4 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 |
---|---|---|---|---|---|---|---|
JCAD | NM_020848.4 | c.3809G>C | p.Arg1270Pro | missense_variant | 3/4 | ENST00000375377.2 | |
JCAD | NM_001350022.2 | c.3809G>C | p.Arg1270Pro | missense_variant | 4/5 | ||
JCAD | NM_001350001.2 | c.3395G>C | p.Arg1132Pro | missense_variant | 4/5 | ||
JCAD | NM_001350021.2 | c.3395G>C | p.Arg1132Pro | missense_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
JCAD | ENST00000375377.2 | c.3809G>C | p.Arg1270Pro | missense_variant | 3/4 | 5 | NM_020848.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249452Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135344
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461824Hom.: 0 Cov.: 30 AF XY: 0.00000550 AC XY: 4AN XY: 727226
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 28, 2024 | The c.3809G>C (p.R1270P) alteration is located in exon 3 (coding exon 2) of the KIAA1462 gene. This alteration results from a G to C substitution at nucleotide position 3809, causing the arginine (R) at amino acid position 1270 to be replaced by a proline (P). 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