chr17-28616981-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP2
The NM_014680.5(BLTP2):c.5929A>T(p.Ser1977Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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. S1977N) has been classified as Uncertain significance.
Frequency
Consequence
NM_014680.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BLTP2 | NM_014680.5 | c.5929A>T | p.Ser1977Cys | missense_variant | 34/39 | ENST00000528896.7 | |
SPAG5-AS1 | NR_040012.1 | n.969T>A | non_coding_transcript_exon_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BLTP2 | ENST00000528896.7 | c.5929A>T | p.Ser1977Cys | missense_variant | 34/39 | 1 | NM_014680.5 | P1 | |
SPAG5-AS1 | ENST00000414744.2 | n.1747T>A | non_coding_transcript_exon_variant | 2/2 | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 12, 2023 | The c.5929A>T (p.S1977C) alteration is located in exon 34 (coding exon 34) of the KIAA0100 gene. This alteration results from a A to T substitution at nucleotide position 5929, causing the serine (S) at amino acid position 1977 to be replaced by a cysteine (C). 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
Publications
No publications associated with this variant yet.