Variant chr15-43635172-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.1178+188A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 650,816 control chromosomes in the GnomAD database, including 8,463 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.13 ( 1673 hom., cov: 29)

Exomes 𝑓: 0.15 ( 6790 hom. )

Consequence

CATSPER2
NM_172095.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.729

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=-0.87).

BP6

Variant 15-43635172-T-C is Benign according to our data. Variant chr15-43635172-T-C is described in ClinVar as [Benign]. Clinvar id is 1268473.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.1178+188A>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.1178+188A>G		intron_variant		2	NM_172095.4	ENSP00000380088.3		Q96P56-1

Frequencies

GnomAD3 genomes

AF:

0.133

AC:

19901

AN:

149816

Hom.:

1672

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0810

Gnomad AMI

AF:

0.118

Gnomad AMR

AF:

0.128

Gnomad ASJ

AF:

0.187

Gnomad EAS

AF:

0.00137

Gnomad SAS

AF:

0.150

Gnomad FIN

AF:

0.101

Gnomad MID

AF:

0.247

Gnomad NFE

AF:

0.175

Gnomad OTH

AF:

0.147

GnomAD3 exomes

AF:

0.126

AC:

16707

AN:

133014

Hom.:

1385

AF XY:

0.130

AC XY:

9246

AN XY:

71156

show subpopulations

Gnomad AFR exome

AF:

0.0716

Gnomad AMR exome

AF:

0.103

Gnomad ASJ exome

AF:

0.165

Gnomad EAS exome

AF:

0.00294

Gnomad SAS exome

AF:

0.159

Gnomad FIN exome

AF:

0.104

Gnomad NFE exome

AF:

0.158

Gnomad OTH exome

AF:

0.144

GnomAD4 exome

AF:

0.148

AC:

73987

AN:

500884

Hom.:

6790

Cov.:

AF XY:

0.151

AC XY:

40448

AN XY:

268400

show subpopulations

Gnomad4 AFR exome

AF:

0.0773

Gnomad4 AMR exome

AF:

0.104

Gnomad4 ASJ exome

AF:

0.181

Gnomad4 EAS exome

AF:

0.00123

Gnomad4 SAS exome

AF:

0.176

Gnomad4 FIN exome

AF:

0.105

Gnomad4 NFE exome

AF:

0.170

Gnomad4 OTH exome

AF:

0.152

GnomAD4 genome

AF:

0.133

AC:

19916

AN:

149932

Hom.:

1673

Cov.:

AF XY:

0.129

AC XY:

9475

AN XY:

73168

show subpopulations

Gnomad4 AFR

AF:

0.0814

Gnomad4 AMR

AF:

0.128

Gnomad4 ASJ

AF:

0.187

Gnomad4 EAS

AF:

0.00137

Gnomad4 SAS

AF:

0.151

Gnomad4 FIN

AF:

0.101

Gnomad4 NFE

AF:

0.175

Gnomad4 OTH

AF:

0.146

Alfa

AF:

0.136

Hom.:

236

Bravo

AF:

0.131

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 10, 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

-0.87

CADD

Benign

DANN

Benign

0.62

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