chr9-5920028-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001017969.3(KIAA2026):c.5968G>A(p.Ala1990Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000561 in 1,613,800 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001017969.3 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 |
---|---|---|---|---|---|---|---|
KIAA2026 | NM_001017969.3 | c.5968G>A | p.Ala1990Thr | missense_variant | 8/8 | ENST00000399933.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIAA2026 | ENST00000399933.8 | c.5968G>A | p.Ala1990Thr | missense_variant | 8/8 | 5 | NM_001017969.3 | P4 | |
KIAA2026 | ENST00000381461.6 | c.5878G>A | p.Ala1960Thr | missense_variant | 7/7 | 5 | A2 | ||
KIAA2026 | ENST00000436015.6 | c.554+516G>A | intron_variant, NMD_transcript_variant | 3 | |||||
KIAA2026 | ENST00000540714.1 | c.*3555G>A | 3_prime_UTR_variant, NMD_transcript_variant | 7/7 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000322 AC: 49AN: 152134Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000237 AC: 59AN: 249140Hom.: 0 AF XY: 0.000200 AC XY: 27AN XY: 135164
GnomAD4 exome AF: 0.000586 AC: 856AN: 1461666Hom.: 1 Cov.: 35 AF XY: 0.000568 AC XY: 413AN XY: 727122
GnomAD4 genome ? AF: 0.000322 AC: 49AN: 152134Hom.: 0 Cov.: 32 AF XY: 0.000283 AC XY: 21AN XY: 74296
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2021 | The c.5968G>A (p.A1990T) alteration is located in exon 8 (coding exon 8) of the KIAA2026 gene. This alteration results from a G to A substitution at nucleotide position 5968, causing the alanine (A) at amino acid position 1990 to be replaced by a threonine (T). 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