chr9-5920021-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001017969.3(KIAA2026):c.5975T>C(p.Val1992Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,613,876 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/18 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.5975T>C | p.Val1992Ala | missense_variant | 8/8 | ENST00000399933.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIAA2026 | ENST00000399933.8 | c.5975T>C | p.Val1992Ala | missense_variant | 8/8 | 5 | NM_001017969.3 | P4 | |
KIAA2026 | ENST00000381461.6 | c.5885T>C | p.Val1962Ala | missense_variant | 7/7 | 5 | A2 | ||
KIAA2026 | ENST00000436015.6 | c.554+523T>C | intron_variant, NMD_transcript_variant | 3 | |||||
KIAA2026 | ENST00000540714.1 | c.*3562T>C | 3_prime_UTR_variant, NMD_transcript_variant | 7/7 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249180Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135192
GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461688Hom.: 0 Cov.: 35 AF XY: 0.00000413 AC XY: 3AN XY: 727130
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152188Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74344
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 04, 2023 | The c.5975T>C (p.V1992A) alteration is located in exon 8 (coding exon 8) of the KIAA2026 gene. This alteration results from a T to C substitution at nucleotide position 5975, causing the valine (V) at amino acid position 1992 to be replaced by an alanine (A). 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