Variant 15-43632484-G-A 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.1397-121C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 1,430,064 control chromosomes in the GnomAD database, including 19,161 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.22 ( 5820 hom., cov: 32)

Exomes 𝑓: 0.12 ( 13341 hom. )

Consequence

CATSPER2
NM_172095.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.0860

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 15-43632484-G-A is Benign according to our data. Variant chr15-43632484-G-A is described in ClinVar as [Benign]. Clinvar id is 1232282.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.47 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.1397-121C>T		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.1397-121C>T		intron_variant		2	NM_172095.4	ENSP00000380088.3		Q96P56-1

Frequencies

GnomAD3 genomes

AF:

0.217

AC:

32852

AN:

151590

Hom.:

5804

Cov.:

show subpopulations

Gnomad AFR

AF:

0.476

Gnomad AMI

AF:

0.106

Gnomad AMR

AF:

0.195

Gnomad ASJ

AF:

0.180

Gnomad EAS

AF:

0.276

Gnomad SAS

AF:

0.195

Gnomad FIN

AF:

0.0405

Gnomad MID

AF:

0.161

Gnomad NFE

AF:

0.0935

Gnomad OTH

AF:

0.190

GnomAD4 exome

AF:

0.118

AC:

150992

AN:

1278356

Hom.:

13341

Cov.:

AF XY:

0.119

AC XY:

76116

AN XY:

640974

show subpopulations

Gnomad4 AFR exome

AF:

0.497

Gnomad4 AMR exome

AF:

0.198

Gnomad4 ASJ exome

AF:

0.185

Gnomad4 EAS exome

AF:

0.269

Gnomad4 SAS exome

AF:

0.174

Gnomad4 FIN exome

AF:

0.0406

Gnomad4 NFE exome

AF:

0.0935

Gnomad4 OTH exome

AF:

0.142

GnomAD4 genome

AF:

0.217

AC:

32915

AN:

151708

Hom.:

5820

Cov.:

AF XY:

0.214

AC XY:

15867

AN XY:

74148

show subpopulations

Gnomad4 AFR

AF:

0.476

Gnomad4 AMR

AF:

0.195

Gnomad4 ASJ

AF:

0.180

Gnomad4 EAS

AF:

0.276

Gnomad4 SAS

AF:

0.194

Gnomad4 FIN

AF:

0.0405

Gnomad4 NFE

AF:

0.0935

Gnomad4 OTH

AF:

0.194

Alfa

AF:

0.147

Hom.:

516

Bravo

AF:

0.244

Asia WGS

AF:

0.242

AC:

841

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	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 10, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

6.4

DANN

Benign

0.77

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