X-119087112-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001394962.1(KIAA1210):c.3590A>T(p.Gln1197Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000892 in 112,128 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. 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 (★).
Frequency
Consequence
NM_001394962.1 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 |
---|---|---|---|---|---|---|---|---|
KIAA1210 | NM_001394962.1 | c.3590A>T | p.Gln1197Leu | missense_variant | 9/12 | ENST00000691062.1 | NP_001381891.1 | |
KIAA1210 | NM_020721.1 | c.4118A>T | p.Gln1373Leu | missense_variant | 11/14 | NP_065772.1 | ||
KIAA1210 | XM_017029688.3 | c.3635A>T | p.Gln1212Leu | missense_variant | 9/12 | XP_016885177.1 | ||
KIAA1210 | XM_017029689.3 | c.3437A>T | p.Gln1146Leu | missense_variant | 8/11 | XP_016885178.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KIAA1210 | ENST00000691062.1 | c.3590A>T | p.Gln1197Leu | missense_variant | 9/12 | NM_001394962.1 | ENSP00000510348.1 | |||
KIAA1210 | ENST00000402510.2 | c.4118A>T | p.Gln1373Leu | missense_variant | 11/14 | 5 | ENSP00000384670.2 |
Frequencies
GnomAD3 genomes AF: 0.00000892 AC: 1AN: 112128Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 34284
GnomAD3 exomes AF: 0.00000551 AC: 1AN: 181371Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67363
GnomAD4 exome Cov.: 32
GnomAD4 genome AF: 0.00000892 AC: 1AN: 112128Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 34284
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 16, 2024 | The c.4118A>T (p.Q1373L) alteration is located in exon 11 (coding exon 11) of the KIAA1210 gene. This alteration results from a A to T substitution at nucleotide position 4118, causing the glutamine (Q) at amino acid position 1373 to be replaced by a leucine (L). 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