6-27815068-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003521.3(H2BC14):c.25C>T(p.Pro9Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000236 in 1,612,802 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003521.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152106Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000440 AC: 11AN: 250150Hom.: 0 AF XY: 0.0000370 AC XY: 5AN XY: 135194
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1460578Hom.: 0 Cov.: 32 AF XY: 0.0000193 AC XY: 14AN XY: 726620
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152224Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74414
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.25C>T (p.P9S) alteration is located in exon 1 (coding exon 1) of the HIST1H2BM gene. This alteration results from a C to T substitution at nucleotide position 25, causing the proline (P) at amino acid position 9 to be replaced by a serine (S). 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