rs200981
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_003511.3(H2AC16):āc.42A>Gā(p.Lys14Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 1,611,568 control chromosomes in the GnomAD database, including 12,839 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: š 0.12 ( 1325 hom., cov: 32)
Exomes š: 0.12 ( 11514 hom. )
Consequence
H2AC16
NM_003511.3 synonymous
NM_003511.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.17
Genes affected
H2AC16 (HGNC:4730): (H2A clustered histone 16) Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Two molecules of each of the four core histones (H2A, H2B, H3, and H4) form an octamer, around which approximately 146 bp of DNA is wrapped in repeating units, called nucleosomes. The linker histone, H1, interacts with linker DNA between nucleosomes and functions in the compaction of chromatin into higher order structures. This gene is intronless and encodes a replication-dependent histone that is a member of the histone H2A family. Transcripts from this gene lack polyA tails but instead contain a palindromic termination element. This gene is found in the small histone gene cluster on chromosome 6p22-p21.3. [provided by RefSeq, Aug 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.69).
BP7
Synonymous conserved (PhyloP=3.16 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
H2AC16 | NM_003511.3 | c.42A>G | p.Lys14Lys | synonymous_variant | 1/1 | ENST00000613174.2 | NP_003502.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
H2AC16 | ENST00000613174.2 | c.42A>G | p.Lys14Lys | synonymous_variant | 1/1 | 6 | NM_003511.3 | ENSP00000482538.2 |
Frequencies
GnomAD3 genomes AF: 0.123 AC: 18728AN: 151994Hom.: 1318 Cov.: 32
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GnomAD3 exomes AF: 0.103 AC: 25819AN: 250236Hom.: 1590 AF XY: 0.102 AC XY: 13850AN XY: 135310
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GnomAD4 exome AF: 0.120 AC: 175666AN: 1459456Hom.: 11514 Cov.: 32 AF XY: 0.119 AC XY: 86245AN XY: 725572
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GnomAD4 genome AF: 0.123 AC: 18764AN: 152112Hom.: 1325 Cov.: 32 AF XY: 0.119 AC XY: 8869AN XY: 74364
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at