Variant rs3813131 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_032436.4(CHAMP1):c.702G>A(p.Pro234Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.099 in 1,613,838 control chromosomes in the GnomAD database, including 10,694 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.15 ( 2462 hom., cov: 32)

Exomes 𝑓: 0.093 ( 8232 hom. )

Consequence

CHAMP1
NM_032436.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.44

Variant links:

Genes affected

CHAMP1 (HGNC:20311): (chromosome alignment maintaining phosphoprotein 1) This gene encodes a zinc finger protein that functions as a regulator of chromosome segregation in mitosis. The encoded protein is required for correct alignment of chromosomes on the metaphase plate, and plays a role in maintaining the attachment of sister kinetochores to microtubules from opposite spindle poles. Mutations in this gene are associated with an autosomal dominant form of intellectual disability. [provided by RefSeq, Jul 2017]

CHAMP1 links:

CHAMP1 (HGNC:):

CHAMP1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP7

Synonymous conserved (PhyloP=-1.44 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CHAMP1	NM_032436.4 linkuse as main transcript	c.702G>A	p.Pro234Pro	synonymous_variant	3/3	ENST00000361283.4	NP_115812.1	Q96JM3
CHAMP1	NM_001164144.3 linkuse as main transcript	c.702G>A	p.Pro234Pro	synonymous_variant	3/3		NP_001157616.1	Q96JM3
CHAMP1	NM_001164145.3 linkuse as main transcript	c.702G>A	p.Pro234Pro	synonymous_variant	3/3		NP_001157617.1	Q96JM3
CHAMP1	XM_047430277.1 linkuse as main transcript	c.702G>A	p.Pro234Pro	synonymous_variant	3/3		XP_047286233.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CHAMP1	ENST00000361283.4 linkuse as main transcript	c.702G>A	p.Pro234Pro	synonymous_variant	3/3	1	NM_032436.4	ENSP00000354730.1		Q96JM3

Frequencies

GnomAD3 genomes

AF:

0.152

AC:

23103

AN:

151834

Hom.:

2455

Cov.:

show subpopulations

Gnomad AFR

AF:

0.298

Gnomad AMI

AF:

0.0308

Gnomad AMR

AF:

0.172

Gnomad ASJ

AF:

0.134

Gnomad EAS

AF:

0.119

Gnomad SAS

AF:

0.151

Gnomad FIN

AF:

0.0830

Gnomad MID

AF:

0.165

Gnomad NFE

AF:

0.0749

Gnomad OTH

AF:

0.150

GnomAD3 exomes

AF:

0.126

AC:

31622

AN:

251438

Hom.:

2654

AF XY:

0.119

AC XY:

16227

AN XY:

135902

show subpopulations

Gnomad AFR exome

AF:

0.305

Gnomad AMR exome

AF:

0.219

Gnomad ASJ exome

AF:

0.128

Gnomad EAS exome

AF:

0.106

Gnomad SAS exome

AF:

0.146

Gnomad FIN exome

AF:

0.0812

Gnomad NFE exome

AF:

0.0780

Gnomad OTH exome

AF:

0.119

GnomAD4 exome

AF:

0.0935

AC:

136656

AN:

1461886

Hom.:

8232

Cov.:

AF XY:

0.0940

AC XY:

68371

AN XY:

727248

show subpopulations

Gnomad4 AFR exome

AF:

0.306

Gnomad4 AMR exome

AF:

0.215

Gnomad4 ASJ exome

AF:

0.132

Gnomad4 EAS exome

AF:

0.146

Gnomad4 SAS exome

AF:

0.145

Gnomad4 FIN exome

AF:

0.0796

Gnomad4 NFE exome

AF:

0.0748

Gnomad4 OTH exome

AF:

0.110

GnomAD4 genome

AF:

0.152

AC:

23144

AN:

151952

Hom.:

2462

Cov.:

AF XY:

0.152

AC XY:

11302

AN XY:

74282

show subpopulations

Gnomad4 AFR

AF:

0.298

Gnomad4 AMR

AF:

0.172

Gnomad4 ASJ

AF:

0.134

Gnomad4 EAS

AF:

0.120

Gnomad4 SAS

AF:

0.149

Gnomad4 FIN

AF:

0.0830

Gnomad4 NFE

AF:

0.0749

Gnomad4 OTH

AF:

0.151

Alfa

AF:

0.0967

Hom.:

1948

Bravo

AF:

0.165

Asia WGS

AF:

0.167

AC:

580

AN:

3478

EpiCase

AF:

0.0816

EpiControl

AF:

0.0805

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

5.6

DANN

Benign

0.36

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over