8-42966532-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_032410.4(HOOK3):c.839C>T(p.Ser280Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,832 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032410.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HOOK3 | ENST00000307602.9 | c.839C>T | p.Ser280Phe | missense_variant | Exon 10 of 22 | 1 | NM_032410.4 | ENSP00000305699.3 | ||
HOOK3 | ENST00000527306.1 | n.1025C>T | non_coding_transcript_exon_variant | Exon 10 of 16 | 1 | |||||
HOOK3 | ENST00000533539.2 | c.839C>T | p.Ser280Phe | missense_variant | Exon 10 of 23 | 3 | ENSP00000433953.2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251456Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135896
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461832Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 727228
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.839C>T (p.S280F) alteration is located in exon 10 (coding exon 10) of the HOOK3 gene. This alteration results from a C to T substitution at nucleotide position 839, causing the serine (S) at amino acid position 280 to be replaced by a phenylalanine (F). 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