chr6-26183815-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 4P and 4B. PM1PM2BP4_Strong
The NM_003523.3(H2BC6):c.20C>A(p.Ser7Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.000211 in 1,607,094 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 9/15 in silico tools predict a benign outcome for this variant. 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. S7C) has been classified as Uncertain significance.
Frequency
Consequence
NM_003523.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
H2BC6 | NM_003523.3 | c.20C>A | p.Ser7Tyr | missense_variant | 1/1 | ENST00000614097.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
H2BC6 | ENST00000614097.3 | c.20C>A | p.Ser7Tyr | missense_variant | 1/1 | NM_003523.3 | P1 | ||
ENST00000707189.1 | n.999+59644C>A | intron_variant, non_coding_transcript_variant | |||||||
ENST00000707191.1 | n.1000+25694C>A | intron_variant, non_coding_transcript_variant | |||||||
H2BC6 | ENST00000634910.1 | c.20C>A | p.Ser7Tyr | missense_variant | 4/4 | 5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000237 AC: 36AN: 151766Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000426 AC: 107AN: 251446Hom.: 0 AF XY: 0.000383 AC XY: 52AN XY: 135898
GnomAD4 exome AF: 0.000208 AC: 303AN: 1455328Hom.: 1 Cov.: 30 AF XY: 0.000213 AC XY: 154AN XY: 724034
GnomAD4 genome AF: 0.000237 AC: 36AN: 151766Hom.: 0 Cov.: 32 AF XY: 0.000297 AC XY: 22AN XY: 74174
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 01, 2021 | The c.20C>A (p.S7Y) alteration is located in exon 1 (coding exon 1) of the HIST1H2BE gene. This alteration results from a C to A substitution at nucleotide position 20, causing the serine (S) at amino acid position 7 to be replaced by a tyrosine (Y). 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