11-66016764-ACT-A

Position:

• chr11-66016764-ACT-A

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_053054.4(CATSPER1):​c.*124_*125delAG variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00236 in 1,070,490 control chromosomes in the GnomAD database, including 6 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.0015 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0025 (6 hom.)
• Consequence: CATSPER1 NM_053054.4 3_prime_UTR
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 1.23

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 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BS2: High Homozygotes in GnomAdExome4 at 6 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CATSPER1	NM_053054.4	c.*124_*125delAG		3_prime_UTR_variant	12/12	ENST00000312106.6	NP_444282.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CATSPER1	ENST00000312106	c.*124_*125delAG		3_prime_UTR_variant	12/12	1	NM_053054.4	ENSP00000309052.5
CATSPER1	ENST00000529244.1	n.707_708delAG		non_coding_transcript_exon_variant	6/6	3

Frequencies

GnomAD3 genomes AF: 0.00149 AC: 225 AN: 151048 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000854

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000526

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000286

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00257

Gnomad OTH AF: 0.00240

GnomAD4 exome AF: 0.00251 AC: 2305 AN: 919442 Hom.: 6 AF XY: 0.00244 AC XY: 1133 AN XY: 464920

Gnomad4 AFR exome AF: 0.000516

Gnomad4 AMR exome AF: 0.000198

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000506

Gnomad4 FIN exome AF: 0.000542

Gnomad4 NFE exome AF: 0.00325

Gnomad4 OTH exome AF: 0.00213

GnomAD4 genome AF: 0.00149 AC: 225 AN: 151048 Hom.: 0 Cov.: 32 AF XY: 0.00110 AC XY: 81 AN XY: 73682

Gnomad4 AFR AF: 0.000854

Gnomad4 AMR AF: 0.000526

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000286

Gnomad4 NFE AF: 0.00257

Gnomad4 OTH AF: 0.00240

Alfa AF: 0.00254 Hom.: 0

Bravo AF: 0.00170

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Male infertility Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs764701805; hg19: chr11-65784235;