chr6-26123826-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_003526.3(H2BC4):c.79G>A(p.Gly27Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000088 in 1,614,146 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_003526.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
H2BC4 | NM_003526.3 | c.79G>A | p.Gly27Ser | missense_variant | 1/1 | ENST00000396984.2 | |
H2BC4 | NM_001381989.1 | c.79G>A | p.Gly27Ser | missense_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
H2BC4 | ENST00000396984.2 | c.79G>A | p.Gly27Ser | missense_variant | 1/1 | NM_003526.3 | P1 | ||
H2BC4 | ENST00000314332.5 | c.79G>A | p.Gly27Ser | missense_variant | 1/2 | 1 | P1 | ||
ENST00000707189.1 | n.654C>T | non_coding_transcript_exon_variant | 1/2 | ||||||
H2BC4 | ENST00000707188.1 | c.79G>A | p.Gly27Ser | missense_variant, NMD_transcript_variant | 1/3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000722 AC: 11AN: 152254Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000676 AC: 17AN: 251490Hom.: 0 AF XY: 0.0000809 AC XY: 11AN XY: 135920
GnomAD4 exome AF: 0.0000896 AC: 131AN: 1461892Hom.: 0 Cov.: 32 AF XY: 0.0000798 AC XY: 58AN XY: 727248
GnomAD4 genome ? AF: 0.0000722 AC: 11AN: 152254Hom.: 0 Cov.: 33 AF XY: 0.0000806 AC XY: 6AN XY: 74396
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 11, 2021 | The c.79G>A (p.G27S) alteration is located in exon 1 (coding exon 1) of the HIST1H2BC gene. This alteration results from a G to A substitution at nucleotide position 79, causing the glycine (G) at amino acid position 27 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