Variant 15-43632151-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_172095.4(CATSPER2):c.1561+48G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00754 in 144,570 control chromosomes in the GnomAD database, including 19 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0075 ( 19 hom., cov: 32)

Exomes 𝑓: 0.025 ( 20 hom. )

Failed GnomAD Quality Control

Consequence

CATSPER2
NM_172095.4 intron

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -2.01

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:

ENSG00000284772 (HGNC:):

ENSG00000284772 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=-0.98).

BP6

Variant 15-43632151-C-T is Benign according to our data. Variant chr15-43632151-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1216831.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00754 (1090/144570) while in subpopulation AFR AF= 0.0232 (949/40886). AF 95% confidence interval is 0.022. There are 19 homozygotes in gnomad4. There are 518 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 19 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CATSPER2	NM_172095.4 linkuse as main transcript	c.1561+48G>A		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.1561+48G>A		intron_variant		2	NM_172095.4	ENSP00000380088.3		Q96P56-1
ENSG00000284772	ENST00000643290.1 linkuse as main transcript	n.85+48G>A		intron_variant				ENSP00000495476.1		A0A2R8Y6Q2

Frequencies

GnomAD3 genomes

AF:

0.00752

AC:

1087

AN:

144456

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0232

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00337

Gnomad ASJ

AF:

0.00220

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00195

Gnomad FIN

AF:

0.000399

Gnomad MID

AF:

0.0133

Gnomad NFE

AF:

0.000886

Gnomad OTH

AF:

0.00617

GnomAD3 exomes

AF:

0.00382

AC:

896

AN:

234394

Hom.:

AF XY:

0.00326

AC XY:

412

AN XY:

126206

show subpopulations

Gnomad AFR exome

AF:

0.0223

Gnomad AMR exome

AF:

0.00276

Gnomad ASJ exome

AF:

0.00832

Gnomad EAS exome

AF:

0.00204

Gnomad SAS exome

AF:

0.00192

Gnomad FIN exome

AF:

0.000930

Gnomad NFE exome

AF:

0.00233

Gnomad OTH exome

AF:

0.00352

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0248

AC:

29834

AN:

1203422

Hom.:

Cov.:

AF XY:

0.0230

AC XY:

13898

AN XY:

603004

show subpopulations

Gnomad4 AFR exome

AF:

0.0234

Gnomad4 AMR exome

AF:

0.00600

Gnomad4 ASJ exome

AF:

0.0164

Gnomad4 EAS exome

AF:

0.00345

Gnomad4 SAS exome

AF:

0.00701

Gnomad4 FIN exome

AF:

0.00260

Gnomad4 NFE exome

AF:

0.0298

Gnomad4 OTH exome

AF:

0.0196

GnomAD4 genome

AF:

0.00754

AC:

1090

AN:

144570

Hom.:

Cov.:

AF XY:

0.00734

AC XY:

518

AN XY:

70598

show subpopulations

Gnomad4 AFR

AF:

0.0232

Gnomad4 AMR

AF:

0.00336

Gnomad4 ASJ

AF:

0.00220

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00195

Gnomad4 FIN

AF:

0.000399

Gnomad4 NFE

AF:

0.000886

Gnomad4 OTH

AF:

0.00610

Alfa

AF:

0.0190

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Likely benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 10, 2018	- -
Likely 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

-0.98

CADD

Benign

0.077

DANN

Benign

0.55

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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