Variant 15-43632410-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_172095.4(CATSPER2):c.1397-47A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 1,603,536 control chromosomes in the GnomAD database, including 24,860 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.15 ( 2010 hom., cov: 32)

Exomes 𝑓: 0.17 ( 22850 hom. )

Consequence

CATSPER2
NM_172095.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.0670

Variant links:

Genes affected

CATSPER2 (HGNC:18810): (cation channel sperm associated 2) This gene encodes a member of a family of cation channel proteins that localize to the flagellum of spermatozoa. Defects at this locus causes male infertility. Alternatively spliced transcript variants have been observed at this locus. Readthrough transcription originates upstream of this locus in diphosphoinositol pentakisphosphate kinase 1 pseudogene 1 and is represented by GeneID:110006325. Related pseudogenes are found next to this locus on chromosome 15 and on chromosome 5. [provided by RefSeq, Mar 2017]

CATSPER2 links:

CATSPER2 (HGNC:):

CATSPER2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

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

BP6

Variant 15-43632410-T-C is Benign according to our data. Variant chr15-43632410-T-C is described in ClinVar as [Benign]. Clinvar id is 1257419.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CATSPER2	NM_172095.4 linkuse as main transcript	c.1397-47A>G		intron_variant		ENST00000396879.8	NP_742093.1	Q96P56-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CATSPER2	ENST00000396879.8 linkuse as main transcript	c.1397-47A>G		intron_variant		2	NM_172095.4	ENSP00000380088.3		Q96P56-1

Frequencies

GnomAD3 genomes

AF:

0.151

AC:

22799

AN:

151484

Hom.:

2009

Cov.:

show subpopulations

Gnomad AFR

AF:

0.143

Gnomad AMI

AF:

0.116

Gnomad AMR

AF:

0.133

Gnomad ASJ

AF:

0.187

Gnomad EAS

AF:

0.00155

Gnomad SAS

AF:

0.153

Gnomad FIN

AF:

0.103

Gnomad MID

AF:

0.250

Gnomad NFE

AF:

0.175

Gnomad OTH

AF:

0.159

GnomAD3 exomes

AF:

0.142

AC:

34858

AN:

245056

Hom.:

3049

AF XY:

0.148

AC XY:

19714

AN XY:

133128

show subpopulations

Gnomad AFR exome

AF:

0.134

Gnomad AMR exome

AF:

0.0942

Gnomad ASJ exome

AF:

0.190

Gnomad EAS exome

AF:

0.00303

Gnomad SAS exome

AF:

0.174

Gnomad FIN exome

AF:

0.106

Gnomad NFE exome

AF:

0.173

Gnomad OTH exome

AF:

0.162

GnomAD4 exome

AF:

0.165

AC:

240150

AN:

1451936

Hom.:

22850

Cov.:

AF XY:

0.166

AC XY:

120275

AN XY:

722620

show subpopulations

Gnomad4 AFR exome

AF:

0.138

Gnomad4 AMR exome

AF:

0.0986

Gnomad4 ASJ exome

AF:

0.189

Gnomad4 EAS exome

AF:

0.00141

Gnomad4 SAS exome

AF:

0.180

Gnomad4 FIN exome

AF:

0.107

Gnomad4 NFE exome

AF:

0.176

Gnomad4 OTH exome

AF:

0.162

GnomAD4 genome

AF:

0.151

AC:

22817

AN:

151600

Hom.:

2010

Cov.:

AF XY:

0.147

AC XY:

10875

AN XY:

74070

show subpopulations

Gnomad4 AFR

AF:

0.143

Gnomad4 AMR

AF:

0.132

Gnomad4 ASJ

AF:

0.187

Gnomad4 EAS

AF:

0.00155

Gnomad4 SAS

AF:

0.153

Gnomad4 FIN

AF:

0.103

Gnomad4 NFE

AF:

0.175

Gnomad4 OTH

AF:

0.157

Alfa

AF:

0.168

Hom.:

437

Bravo

AF:

0.151

Asia WGS

AF:

0.0740

AC:

260

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 11, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

6.3

DANN

Benign

0.60

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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