Variant 11-66020296-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_StrongBA1

The NM_053054.4(CATSPER1):c.2064+21G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00488 in 1,614,152 control chromosomes in the GnomAD database, including 261 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.012 ( 50 hom., cov: 32)

Exomes 𝑓: 0.0041 ( 211 hom. )

Consequence

CATSPER1
NM_053054.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.980

Variant links:

Genes affected

CATSPER1 (HGNC:17116): (cation channel sperm associated 1) Calcium ions play a primary role in the regulation of sperm motility. This gene belongs to a family of putative cation channels that are specific to spermatozoa and localize to the flagellum. The protein family features a single repeat with six membrane-spanning segments and a predicted calcium-selective pore region. [provided by RefSeq, Jul 2008]

CATSPER1 links:

CATSPER1 (HGNC:):

CATSPER1 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=-0.72).

BP6

Variant 11-66020296-C-T is Benign according to our data. Variant chr11-66020296-C-T is described in ClinVar as [Benign]. Clinvar id is 1239201.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.1 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
CATSPER1	NM_053054.4 linkuse as main transcript	c.2064+21G>A	intron_variant	ENST00000312106.6	NP_444282.3	Q8NEC5
CATSPER1	XM_047426337.1 linkuse as main transcript	c.2064+21G>A	intron_variant		XP_047282293.1
CATSPER1	XR_002957121.2 linkuse as main transcript	n.2100+21G>A	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CATSPER1	ENST00000312106.6 linkuse as main transcript	c.2064+21G>A		intron_variant		1	NM_053054.4	ENSP00000309052.5		Q8NEC5
CATSPER1	ENST00000529244.1 linkuse as main transcript	n.266-96G>A		intron_variant		3

Frequencies

GnomAD3 genomes

AF:

0.0120

AC:

1823

AN:

152208

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0245

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0113

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.108

Gnomad SAS

AF:

0.00703

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.000309

Gnomad OTH

AF:

0.00813

GnomAD3 exomes

AF:

0.0123

AC:

3093

AN:

251338

Hom.:

132

AF XY:

0.0104

AC XY:

1409

AN XY:

135828

show subpopulations

Gnomad AFR exome

AF:

0.0249

Gnomad AMR exome

AF:

0.0150

Gnomad ASJ exome

AF:

0.000397

Gnomad EAS exome

AF:

0.109

Gnomad SAS exome

AF:

0.00317

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000229

Gnomad OTH exome

AF:

0.00685

GnomAD4 exome

AF:

0.00414

AC:

6048

AN:

1461826

Hom.:

211

Cov.:

AF XY:

0.00389

AC XY:

2826

AN XY:

727212

show subpopulations

Gnomad4 AFR exome

AF:

0.0238

Gnomad4 AMR exome

AF:

0.0143

Gnomad4 ASJ exome

AF:

0.000650

Gnomad4 EAS exome

AF:

0.0915

Gnomad4 SAS exome

AF:

0.00339

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000142

Gnomad4 OTH exome

AF:

0.00811

GnomAD4 genome

AF:

0.0120

AC:

1828

AN:

152326

Hom.:

Cov.:

AF XY:

0.0123

AC XY:

918

AN XY:

74484

show subpopulations

Gnomad4 AFR

AF:

0.0245

Gnomad4 AMR

AF:

0.0118

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.108

Gnomad4 SAS

AF:

0.00704

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000309

Gnomad4 OTH

AF:

0.00804

Alfa

AF:

0.00590

Hom.:

Bravo

AF:

0.0148

Asia WGS

AF:

0.0460

AC:

160

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	Jun 19, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.72

CADD

Benign

5.3

DANN

Benign

0.86

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