6-26225270-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_003532.3(H3C6):c.116C>T(p.Pro39Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000342 in 1,461,728 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003532.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
H3C6 | ENST00000614911.3 | c.116C>T | p.Pro39Leu | missense_variant | Exon 1 of 1 | 6 | NM_003532.3 | ENSP00000482271.1 | ||
H3C6 | ENST00000634733.1 | c.116C>T | p.Pro39Leu | missense_variant | Exon 2 of 2 | 1 | ENSP00000489282.1 | |||
ENSG00000291336 | ENST00000707189.1 | n.999+101099C>T | intron_variant | Intron 1 of 1 | ||||||
ENSG00000291338 | ENST00000707191.1 | n.1000+67149C>T | intron_variant | Intron 1 of 1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251178Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135764
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461728Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 2AN XY: 727168
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.116C>T (p.P39L) alteration is located in exon 1 (coding exon 1) of the HIST1H3E gene. This alteration results from a C to T substitution at nucleotide position 116, causing the proline (P) at amino acid position 39 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