6-27838858-T-G

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_003520.4(H2BC15):c.197T>G(p.Phe66Cys) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: H2BC15 NM_003520.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 3.97

Genes affected

H2BC15 (HGNC:4749): (H2B clustered histone 15) 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 H2B 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]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
H2BC15	NM_003520.4	c.197T>G	p.Phe66Cys	missense_variant	1/1	ENST00000612898.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
H2BC15	ENST00000612898.2	c.197T>G	p.Phe66Cys	missense_variant	1/1		NM_003520.4	P1
H2BC15	ENST00000606613.1	c.197T>G	p.Phe66Cys	missense_variant	1/3	1
H2BC15	ENST00000449538.3	c.197T>G	p.Phe66Cys	missense_variant, NMD_transcript_variant	1/3	1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Feb 28, 2023

The c.197T>G (p.F66C) alteration is located in exon 1 (coding exon 1) of the HIST1H2BN gene. This alteration results from a T to G substitution at nucleotide position 197, causing the phenylalanine (F) at amino acid position 66 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.99
BayesDel_addAF	Pathogenic	0.19	D
BayesDel_noAF	Uncertain	0.040
Cadd	Uncertain	23
Dann	Benign	0.88
DEOGEN2	Uncertain	0.43	T;T;T
Eigen	Uncertain	0.48
Eigen_PC	Uncertain	0.41
FATHMM_MKL	Benign	0.62	D
M_CAP	Benign	0.0086	T
MetaRNN	Uncertain	0.66	D;D;D
MetaSVM	Benign	-0.79	T
MutationAssessor	Pathogenic	3.7	H;.;H
MutationTaster	Benign	0.89	N;N
PrimateAI	Pathogenic	0.93	D
Sift4G	Pathogenic	0.0	D;D;D
Polyphen		0.22	B;.;B
Vest4		0.56
MutPred		0.74		Loss of stability (P = 0.0306);Loss of stability (P = 0.0306);Loss of stability (P = 0.0306);
MVP		0.48
MPC		1.7
ClinPred		0.97	D
GERP RS		3.4
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.3
Varity_R		0.51
gMVP		0.55

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr6-27806636;