Variant 15-43632937-T-G 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.1179-3A>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 150,672 control chromosomes in the GnomAD database, including 15,168 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.40 ( 15168 hom., cov: 30)

Exomes 𝑓: 0.29 ( 67450 hom. )

Failed GnomAD Quality Control

Consequence

CATSPER2
NM_172095.4 splice_region, intron

Scores

Splicing: ADA: 0.00004899

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.507

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=-0.99).

BP6

Variant 15-43632937-T-G is Benign according to our data. Variant chr15-43632937-T-G is described in ClinVar as [Benign]. Clinvar id is 517822.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.704 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.1179-3A>C		splice_region_variant, 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.1179-3A>C		splice_region_variant, intron_variant		2	NM_172095.4	ENSP00000380088.3		Q96P56-1

Frequencies

GnomAD3 genomes

AF:

0.399

AC:

60079

AN:

150562

Hom.:

15124

Cov.:

show subpopulations

Gnomad AFR

AF:

0.710

Gnomad AMI

AF:

0.221

Gnomad AMR

AF:

0.340

Gnomad ASJ

AF:

0.373

Gnomad EAS

AF:

0.324

Gnomad SAS

AF:

0.355

Gnomad FIN

AF:

0.178

Gnomad MID

AF:

0.436

Gnomad NFE

AF:

0.273

Gnomad OTH

AF:

0.375

GnomAD3 exomes

AF:

0.317

AC:

77675

AN:

244874

Hom.:

13944

AF XY:

0.314

AC XY:

41725

AN XY:

133062

show subpopulations

Gnomad AFR exome

AF:

0.713

Gnomad AMR exome

AF:

0.301

Gnomad ASJ exome

AF:

0.381

Gnomad EAS exome

AF:

0.329

Gnomad SAS exome

AF:

0.362

Gnomad FIN exome

AF:

0.180

Gnomad NFE exome

AF:

0.274

Gnomad OTH exome

AF:

0.305

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.291

AC:

415379

AN:

1427870

Hom.:

67450

Cov.:

AF XY:

0.293

AC XY:

208345

AN XY:

711740

show subpopulations

Gnomad4 AFR exome

AF:

0.728

Gnomad4 AMR exome

AF:

0.305

Gnomad4 ASJ exome

AF:

0.379

Gnomad4 EAS exome

AF:

0.332

Gnomad4 SAS exome

AF:

0.364

Gnomad4 FIN exome

AF:

0.181

Gnomad4 NFE exome

AF:

0.271

Gnomad4 OTH exome

AF:

0.317

GnomAD4 genome

AF:

0.399

AC:

60173

AN:

150672

Hom.:

15168

Cov.:

AF XY:

0.394

AC XY:

28984

AN XY:

73626

show subpopulations

Gnomad4 AFR

AF:

0.711

Gnomad4 AMR

AF:

0.340

Gnomad4 ASJ

AF:

0.373

Gnomad4 EAS

AF:

0.324

Gnomad4 SAS

AF:

0.356

Gnomad4 FIN

AF:

0.178

Gnomad4 NFE

AF:

0.273

Gnomad4 OTH

AF:

0.376

Alfa

AF:

0.349

Hom.:

1868

Bravo

AF:

0.429

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 09, 2017

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Rare genetic deafness

Benign:1

Benign, criteria provided, single submitter

clinical testing

Mendelics

May 28, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.60

DANN

Benign

0.48

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000049

dbscSNV1_RF

Benign

0.020

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