16-67842863-GCAGCAGCAGCAA-G

Position:

• chr16-67842863-GCAGCAGCAGCAA-G

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_Moderate BS2

The NM_020457.3(THAP11):​c.321_332delACAGCAGCAGCA​(p.Gln108_Gln111del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.000216 in 1,609,548 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.00019 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00022 (1 hom.)
• Consequence: THAP11 NM_020457.3 disruptive_inframe_deletion
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 4.87

Genes affected

THAP11 (HGNC:23194): (THAP domain containing 11) The protein encoded by this gene contains a THAP domain, which is a conserved DNA-binding domain that has striking similarity to the site-specific DNA-binding domain (DBD) of Drosophila P element transposases. [provided by RefSeq, Jul 2008]

CENPT (HGNC:25787): (centromere protein T) The centromere is a specialized chromatin domain, present throughout the cell cycle, that acts as a platform on which the transient assembly of the kinetochore occurs during mitosis. All active centromeres are characterized by the presence of long arrays of nucleosomes in which CENPA (MIM 117139) replaces histone H3 (see MIM 601128). CENPT is an additional factor required for centromere assembly (Foltz et al., 2006 [PubMed 16622419]).[supplied by OMIM, Mar 2008]

CENPT (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP6: Variant 16-67842863-GCAGCAGCAGCAA-G is Benign according to our data. Variant chr16-67842863-GCAGCAGCAGCAA-G is described in ClinVar as [Likely_benign]. Clinvar id is 2761174.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High AC in GnomAd4 at 29 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
THAP11	NM_020457.3	c.321_332delACAGCAGCAGCA	p.Gln108_Gln111del	disruptive_inframe_deletion	1/1	ENST00000303596.3	NP_065190.2
CENPT	NM_025082.4	c.-492+4526_-492+4537delTTGCTGCTGCTG		intron_variant		ENST00000562787.6	NP_079358.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
THAP11	ENST00000303596.3	c.321_332delACAGCAGCAGCA	p.Gln108_Gln111del	disruptive_inframe_deletion	1/1	6	NM_020457.3	ENSP00000304689.1
CENPT	ENST00000562787.6	c.-492+4526_-492+4537delTTGCTGCTGCTG		intron_variant		2	NM_025082.4	ENSP00000457810.1

Frequencies

GnomAD3 genomes AF: 0.000191 AC: 29 AN: 151698 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000243

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00105

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.0000943

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000147

Gnomad OTH AF: 0.000480

GnomAD3 exomes AF: 0.000217 AC: 52 AN: 239774 Hom.: 1 AF XY: 0.000182 AC XY: 24 AN XY: 131660

Gnomad AFR exome AF: 0.0000710

Gnomad AMR exome AF: 0.000700

Gnomad ASJ exome AF: 0.000102

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000235

Gnomad OTH exome AF: 0.000170

GnomAD4 exome AF: 0.000219 AC: 319 AN: 1457748 Hom.: 1 AF XY: 0.000204 AC XY: 148 AN XY: 725290

Gnomad4 AFR exome AF: 0.0000600

Gnomad4 AMR exome AF: 0.000851

Gnomad4 ASJ exome AF: 0.0000383

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000232

Gnomad4 FIN exome AF: 0.0000194

Gnomad4 NFE exome AF: 0.000237

Gnomad4 OTH exome AF: 0.000166

GnomAD4 genome AF: 0.000191 AC: 29 AN: 151800 Hom.: 0 Cov.: 32 AF XY: 0.000162 AC XY: 12 AN XY: 74218

Gnomad4 AFR AF: 0.0000243

Gnomad4 AMR AF: 0.00105

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.0000943

Gnomad4 NFE AF: 0.000147

Gnomad4 OTH AF: 0.000475

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Sep 28, 2023

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1223887002; hg19: chr16-67876766;