Variant chr16-67829548-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_025082.4(CENPT):c.1187-32A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.472 in 1,566,176 control chromosomes in the GnomAD database, including 185,215 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.58 ( 28552 hom., cov: 31)

Exomes 𝑓: 0.46 ( 156663 hom. )

Consequence

CENPT
NM_025082.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.332

Variant links:

Genes affected

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 links:

TSNAXIP1 (HGNC:18586): (translin associated factor X interacting protein 1) Predicted to be involved in cell differentiation and spermatogenesis. Predicted to be located in perinuclear region of cytoplasm. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

TSNAXIP1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 16-67829548-T-C is Benign according to our data. Variant chr16-67829548-T-C is described in ClinVar as [Benign]. Clinvar id is 1209720.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.881 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CENPT	NM_025082.4 linkuse as main transcript	c.1187-32A>G		intron_variant		ENST00000562787.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CENPT	ENST00000562787.6 linkuse as main transcript	c.1187-32A>G		intron_variant		2	NM_025082.4	P1	Q96BT3-1

Frequencies

GnomAD3 genomes

AF:

0.577

AC:

87696

AN:

151860

Hom.:

28501

Cov.:

show subpopulations

Gnomad AFR

AF:

0.888

Gnomad AMI

AF:

0.487

Gnomad AMR

AF:

0.490

Gnomad ASJ

AF:

0.546

Gnomad EAS

AF:

0.148

Gnomad SAS

AF:

0.567

Gnomad FIN

AF:

0.510

Gnomad MID

AF:

0.642

Gnomad NFE

AF:

0.455

Gnomad OTH

AF:

0.553

GnomAD3 exomes

AF:

0.484

AC:

107630

AN:

222164

Hom.:

28526

AF XY:

0.485

AC XY:

58983

AN XY:

121682

show subpopulations

Gnomad AFR exome

AF:

0.897

Gnomad AMR exome

AF:

0.425

Gnomad ASJ exome

AF:

0.529

Gnomad EAS exome

AF:

0.140

Gnomad SAS exome

AF:

0.582

Gnomad FIN exome

AF:

0.499

Gnomad NFE exome

AF:

0.464

Gnomad OTH exome

AF:

0.496

GnomAD4 exome

AF:

0.460

AC:

650878

AN:

1414196

Hom.:

156663

Cov.:

AF XY:

0.464

AC XY:

327014

AN XY:

705092

show subpopulations

Gnomad4 AFR exome

AF:

0.907

Gnomad4 AMR exome

AF:

0.438

Gnomad4 ASJ exome

AF:

0.541

Gnomad4 EAS exome

AF:

0.146

Gnomad4 SAS exome

AF:

0.570

Gnomad4 FIN exome

AF:

0.495

Gnomad4 NFE exome

AF:

0.446

Gnomad4 OTH exome

AF:

0.484

GnomAD4 genome

AF:

0.578

AC:

87804

AN:

151980

Hom.:

28552

Cov.:

AF XY:

0.577

AC XY:

42859

AN XY:

74274

show subpopulations

Gnomad4 AFR

AF:

0.888

Gnomad4 AMR

AF:

0.489

Gnomad4 ASJ

AF:

0.546

Gnomad4 EAS

AF:

0.149

Gnomad4 SAS

AF:

0.564

Gnomad4 FIN

AF:

0.510

Gnomad4 NFE

AF:

0.455

Gnomad4 OTH

AF:

0.558

Alfa

AF:

0.492

Hom.:

21378

Bravo

AF:

0.583

Asia WGS

AF:

0.455

AC:

1586

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Short stature and microcephaly with genital anomalies

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 22, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.7

DANN

Benign

0.41

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over