Variant 1-193125238-TTATC-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The ENST00000367435.5(CDC73):c.237+29_237+32del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0474 in 1,331,598 control chromosomes in the GnomAD database, including 5,691 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.047 ( 734 hom., cov: 32)

Exomes 𝑓: 0.047 ( 4957 hom. )

Consequence

CDC73
ENST00000367435.5 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.263

Variant links:

Genes affected

CDC73 (HGNC:16783): (cell division cycle 73) This gene encodes a tumor suppressor that is involved in transcriptional and post-transcriptional control pathways. The protein is a component of the the PAF protein complex, which associates with the RNA polymerase II subunit POLR2A and with a histone methyltransferase complex. This protein appears to facilitate the association of 3' mRNA processing factors with actively-transcribed chromatin. Mutations in this gene have been linked to hyperparathyroidism-jaw tumor syndrome, familial isolated hyperparathyroidism, and parathyroid carcinoma. [provided by RefSeq, Jul 2009]

CDC73 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 1-193125238-TTATC-T is Benign according to our data. Variant chr1-193125238-TTATC-T is described in ClinVar as [Benign]. Clinvar id is 21684.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDC73	NM_024529.5 linkuse as main transcript	c.237+29_237+32del		intron_variant		ENST00000367435.5	NP_078805.3
CDC73	XM_006711537.5 linkuse as main transcript	c.237+29_237+32del		intron_variant			XP_006711600.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDC73	ENST00000367435.5 linkuse as main transcript	c.237+29_237+32del		intron_variant		1	NM_024529.5	ENSP00000356405	P1

Frequencies

GnomAD3 genomes

AF:

0.0474

AC:

7209

AN:

152160

Hom.:

735

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0104

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0702

Gnomad ASJ

AF:

0.0320

Gnomad EAS

AF:

0.481

Gnomad SAS

AF:

0.0821

Gnomad FIN

AF:

0.0588

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.0290

Gnomad OTH

AF:

0.0468

GnomAD3 exomes

AF:

0.0830

AC:

20784

AN:

250312

Hom.:

2639

AF XY:

0.0794

AC XY:

10742

AN XY:

135374

show subpopulations

Gnomad AFR exome

AF:

0.00947

Gnomad AMR exome

AF:

0.124

Gnomad ASJ exome

AF:

0.0325

Gnomad EAS exome

AF:

0.492

Gnomad SAS exome

AF:

0.0692

Gnomad FIN exome

AF:

0.0601

Gnomad NFE exome

AF:

0.0291

Gnomad OTH exome

AF:

0.0602

GnomAD4 exome

AF:

0.0474

AC:

55937

AN:

1179320

Hom.:

4957

AF XY:

0.0483

AC XY:

29022

AN XY:

601002

show subpopulations

Gnomad4 AFR exome

AF:

0.00723

Gnomad4 AMR exome

AF:

0.122

Gnomad4 ASJ exome

AF:

0.0318

Gnomad4 EAS exome

AF:

0.438

Gnomad4 SAS exome

AF:

0.0685

Gnomad4 FIN exome

AF:

0.0553

Gnomad4 NFE exome

AF:

0.0250

Gnomad4 OTH exome

AF:

0.0559

GnomAD4 genome

AF:

0.0473

AC:

7200

AN:

152278

Hom.:

734

Cov.:

AF XY:

0.0520

AC XY:

3871

AN XY:

74458

show subpopulations

Gnomad4 AFR

AF:

0.0104

Gnomad4 AMR

AF:

0.0704

Gnomad4 ASJ

AF:

0.0320

Gnomad4 EAS

AF:

0.481

Gnomad4 SAS

AF:

0.0815

Gnomad4 FIN

AF:

0.0588

Gnomad4 NFE

AF:

0.0290

Gnomad4 OTH

AF:

0.0459

Alfa

AF:

0.0380

Hom.:

Bravo

AF:

0.0507

Asia WGS

AF:

0.222

AC:

773

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital

Jul 31, 2024

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 03, 2015

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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