16-67842862-GGCAGCAGCAGCAACAGCA-G

Position:

• chr16-67842862-GGCAGCAGCAGCAACAGCA-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.330_347delGCAGCAGCAACAGCAGCA​(p.Gln111_Gln116del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.000344 in 150,964 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.00034 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00041 (0 hom.)
  • Failed GnomAD Quality Control
• 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 16-67842862-GGCAGCAGCAGCAACAGCA-G is Benign according to our data. Variant chr16-67842862-GGCAGCAGCAGCAACAGCA-G is described in ClinVar as [Likely_benign]. Clinvar id is 2866512.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High AC in GnomAd4 at 52 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
THAP11	NM_020457.3	c.330_347delGCAGCAGCAACAGCAGCA	p.Gln111_Gln116del	disruptive_inframe_deletion	1/1	ENST00000303596.3	NP_065190.2
CENPT	NM_025082.4	c.-492+4521_-492+4538delTGCTGTTGCTGCTGCTGC		intron_variant		ENST00000562787.6	NP_079358.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
THAP11	ENST00000303596.3	c.330_347delGCAGCAGCAACAGCAGCA	p.Gln111_Gln116del	disruptive_inframe_deletion	1/1	6	NM_020457.3	ENSP00000304689.1
CENPT	ENST00000562787.6	c.-492+4521_-492+4538delTGCTGTTGCTGCTGCTGC		intron_variant		2	NM_025082.4	ENSP00000457810.1

Frequencies

GnomAD3 genomes AF: 0.000345 AC: 52 AN: 150844 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000268

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000132

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000394

Gnomad SAS AF: 0.000211

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000519

Gnomad OTH AF: 0.000483

GnomAD3 exomes AF: 0.000334 AC: 80 AN: 239172 Hom.: 0 AF XY: 0.000282 AC XY: 37 AN XY: 131384

Gnomad AFR exome AF: 0.000143

Gnomad AMR exome AF: 0.000292

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.000283

Gnomad SAS exome AF: 0.000197

Gnomad FIN exome AF: 0.000143

Gnomad NFE exome AF: 0.000480

Gnomad OTH exome AF: 0.000510

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000414 AC: 603 AN: 1457058 Hom.: 0 AF XY: 0.000389 AC XY: 282 AN XY: 724880

Gnomad4 AFR exome AF: 0.000210

Gnomad4 AMR exome AF: 0.000336

Gnomad4 ASJ exome AF: 0.0000767

Gnomad4 EAS exome AF: 0.000101

Gnomad4 SAS exome AF: 0.000174

Gnomad4 FIN exome AF: 0.0000968

Gnomad4 NFE exome AF: 0.000475

Gnomad4 OTH exome AF: 0.000416

GnomAD4 genome AF: 0.000344 AC: 52 AN: 150964 Hom.: 0 Cov.: 32 AF XY: 0.000298 AC XY: 22 AN XY: 73764

Gnomad4 AFR AF: 0.000267

Gnomad4 AMR AF: 0.000132

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000394

Gnomad4 SAS AF: 0.000211

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000519

Gnomad4 OTH AF: 0.000478

Alfa AF: 0.000144 Hom.: 0

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

Nov 20, 2023

- -

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: rs752755017; hg19: chr16-67876765;