22-50246373-C-A

Position:

• chr22-50246373-C-A

Variant summary

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

The NM_032019.6(HDAC10):​c.1575G>T​(p.Arg525Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,459,434 control chromosomes in the GnomAD database, with no homozygous occurrence. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 34)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: HDAC10 NM_032019.6 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.0530

Genes affected

HDAC10 (HGNC:18128): (histone deacetylase 10) The protein encoded by this gene belongs to the histone deacetylase family, members of which deacetylate lysine residues on the N-terminal part of the core histones. Histone deacetylation modulates chromatin structure, and plays an important role in transcriptional regulation, cell cycle progression, and developmental events. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2011]

HDAC10 (HGNC:):

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	Protein	UniProt
HDAC10	NM_032019.6	c.1575G>T	p.Arg525Ser	missense_variant	17/20	ENST00000216271.10	NP_114408.3
HDAC10	NM_001159286.2	c.1515G>T	p.Arg505Ser	missense_variant	16/19		NP_001152758.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HDAC10	ENST00000216271.10	c.1575G>T	p.Arg525Ser	missense_variant	17/20	1	NM_032019.6	ENSP00000216271.5

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome AF: 0.00000137 AC: 2 AN: 1459434 Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 2 AN XY: 726132

Gnomad4 AFR exome AF: 0.0000299

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.00e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 34

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

May 16, 2023

The c.1575G>T (p.R525S) alteration is located in exon 17 (coding exon 17) of the HDAC10 gene. This alteration results from a G to T substitution at nucleotide position 1575, causing the arginine (R) at amino acid position 525 to be replaced by a serine (S). 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	Benign	0.30
BayesDel_addAF	Uncertain	0.063	T
BayesDel_noAF	Benign	-0.15
CADD	Benign	18
DANN	Benign	0.95
DEOGEN2	Benign	0.022	T;T;.
Eigen	Benign	-0.63
Eigen_PC	Benign	-0.65
FATHMM_MKL	Benign	0.54	D
LIST_S2	Benign	0.85	T;D;D
M_CAP	Benign	0.027	D
MetaRNN	Uncertain	0.49	T;T;T
MetaSVM	Benign	-0.97	T
MutationAssessor	Uncertain	2.6	M;.;.
PrimateAI	Benign	0.38	T
PROVEAN	Benign	-0.36	N;N;N
REVEL	Benign	0.20
Sift	Benign	0.11	T;T;T
Sift4G	Benign	0.54	T;T;T
Polyphen		0.32	B;P;B
Vest4		0.60
MutPred		0.52		Loss of MoRF binding (P = 0.08);.;.;
MVP		0.69
MPC		0.14
ClinPred		0.097	T
GERP RS		0.51
Varity_R		0.084
gMVP		0.49

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1274391018; hg19: chr22-50684802;