dbSNP rs9568: CHP1:c.*2025C>A (chr15-41281414-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_007236.5(CHP1):c.*2025C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 152,540 control chromosomes in the GnomAD database, including 4,846 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 0.25 ( 4835 hom., cov: 32)

Exomes 𝑓: 0.24 ( 11 hom. )

Consequence

CHP1
NM_007236.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0470

Publications

15 publications found

Variant links:

Genes affected

CHP1 (HGNC:17433): (calcineurin like EF-hand protein 1) This gene encodes a phosphoprotein that binds to the Na+/H+ exchanger NHE1. This protein serves as an essential cofactor which supports the physiological activity of NHE family members and may play a role in the mitogenic regulation of NHE1. The protein shares similarity with calcineurin B and calmodulin and it is also known to be an endogenous inhibitor of calcineurin activity. [provided by RefSeq, Jul 2008]

CHP1 Gene-Disease associations (from GenCC):

spastic ataxia 9, autosomal recessive
Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

CHP1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein
CHP1	NM_007236.5 link	c.*2025C>A	3_prime_UTR_variant	Exon 7 of 7	ENST00000334660.10	NP_009167.1
CHP1	XM_047432124.1 link	c.*2025C>A	3_prime_UTR_variant	Exon 6 of 6		XP_047288080.1
CHP1	XM_047432125.1 link	c.*2025C>A	3_prime_UTR_variant	Exon 6 of 6		XP_047288081.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHP1	ENST00000334660.10 link	c.*2025C>A		3_prime_UTR_variant	Exon 7 of 7	1	NM_007236.5	ENSP00000335632.5

Frequencies

GnomAD3 genomes

AF:

0.246

AC:

37456

AN:

151984

Hom.:

4828

Cov.:

show subpopulations

Gnomad AFR

AF:

0.269

Gnomad AMI

AF:

0.345

Gnomad AMR

AF:

0.201

Gnomad ASJ

AF:

0.276

Gnomad EAS

AF:

0.0110

Gnomad SAS

AF:

0.214

Gnomad FIN

AF:

0.264

Gnomad MID

AF:

0.187

Gnomad NFE

AF:

0.258

Gnomad OTH

AF:

0.245

GnomAD4 exome

AF:

0.237

AC:

104

AN:

438

Hom.:

Cov.:

AF XY:

0.231

AC XY:

AN XY:

264

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.233

AC:

AN:

424

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.400

AC:

AN:

Other (OTH)

AF:

0.250

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.246

AC:

37485

AN:

152102

Hom.:

4835

Cov.:

AF XY:

0.245

AC XY:

18245

AN XY:

74348

show subpopulations

African (AFR)

AF:

0.269

AC:

11159

AN:

41486

American (AMR)

AF:

0.201

AC:

3064

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.276

AC:

958

AN:

3468

East Asian (EAS)

AF:

0.0108

AC:

AN:

5186

South Asian (SAS)

AF:

0.214

AC:

1033

AN:

4832

European-Finnish (FIN)

AF:

0.264

AC:

2782

AN:

10552

Middle Eastern (MID)

AF:

0.180

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.258

AC:

17549

AN:

67990

Other (OTH)

AF:

0.244

AC:

516

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1481

2962

4444

5925

7406

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

392

784

1176

1568

1960

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.243

Hom.:

3017

Bravo

AF:

0.242

Asia WGS

AF:

0.144

AC:

504

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

2.1

(source)

DANN

Benign

0.45

PhyloP100

-0.047

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over