dbSNP rs3217060: CATSPERZ:c.*185_*207delGTGACCTTCATTCGGTCACCGCA (chr11-64304830-CGTGACCTTCATTCGGTCACCGCA-C) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001039496.2(CATSPERZ):c.*185_*207delGTGACCTTCATTCGGTCACCGCA variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00103 in 544,824 control chromosomes in the GnomAD database, including 1 homozygotes. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0010 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0010 ( 1 hom. )

Consequence

CATSPERZ
NM_001039496.2 downstream_gene

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.922

Publications

1 publications found

Variant links:

Genes affected

CATSPERZ (HGNC:19231): (catsper channel auxiliary subunit zeta) Predicted to be involved in flagellated sperm motility; male meiotic nuclear division; and sperm capacitation. Located in cytoplasm and sperm principal piece. [provided by Alliance of Genome Resources, Apr 2022]

CATSPERZ links:

KCNK4-CATSPERZ (HGNC:56753): (KCNK4-CATSPERZ readthrough (NMD candidate)) This locus represents naturally occurring readthrough transcription between the neighboring KCNK4 (potassium channel subfamily K member 4) and the downstream TEX40 (testis expressed 40) chromosome 11. The readthrough transcript is a candidate for nonsense-mediated mRNA decay (NMD), and is unlikely to produce a protein product. [provided by RefSeq, Nov 2015]

KCNK4-CATSPERZ links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CATSPERZ	NM_001039496.2 link	c.185_207delGTGACCTTCATTCGGTCACCGCA		downstream_gene_variant		ENST00000328404.8	NP_001034585.1	Q9NTU4
KCNK4-CATSPERZ	NR_133662.1 link	n.62_84delGTGACCTTCATTCGGTCACCGCA		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
CATSPERZ	ENST00000328404.8 link	c.185_207delGTGACCTTCATTCGGTCACCGCA	downstream_gene_variant	1	NM_001039496.2	ENSP00000491717.1	Q9NTU4
KCNK4-CATSPERZ	ENST00000539086.5 link	n.62_84delGTGACCTTCATTCGGTCACCGCA	downstream_gene_variant	1
CATSPERZ	ENST00000539943.1 link	c.185_207delGTGACCTTCATTCGGTCACCGCA	downstream_gene_variant	2		ENSP00000443917.1	F5H186
CATSPERZ	ENST00000535981.1 link	n.82_104delGTGACCTTCATTCGGTCACCGCA	downstream_gene_variant	2

Frequencies

GnomAD3 genomes

AF:

0.00103

AC:

155

AN:

150064

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00146

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000924

Gnomad ASJ

AF:

0.00262

Gnomad EAS

AF:

0.000789

Gnomad SAS

AF:

0.00276

Gnomad FIN

AF:

0.0000958

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000791

Gnomad OTH

AF:

0.000484

GnomAD4 exome

AF:

0.00103

AC:

407

AN:

394644

Hom.:

AF XY:

0.00128

AC XY:

265

AN XY:

207798

show subpopulations

African (AFR)

AF:

0.000791

AC:

AN:

11380

American (AMR)

AF:

0.000320

AC:

AN:

15642

Ashkenazi Jewish (ASJ)

AF:

0.00279

AC:

AN:

11824

East Asian (EAS)

AF:

0.0000371

AC:

AN:

26970

South Asian (SAS)

AF:

0.00451

AC:

174

AN:

38604

European-Finnish (FIN)

AF:

0.0000771

AC:

AN:

25926

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1872

European-Non Finnish (NFE)

AF:

0.000710

AC:

170

AN:

239414

Other (OTH)

AF:

0.000565

AC:

AN:

23012

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.512

Heterozygous variant carriers

103

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00103

AC:

155

AN:

150180

Hom.:

Cov.:

AF XY:

0.00109

AC XY:

AN XY:

73364

show subpopulations

African (AFR)

AF:

0.00146

AC:

AN:

41086

American (AMR)

AF:

0.000923

AC:

AN:

15168

Ashkenazi Jewish (ASJ)

AF:

0.00262

AC:

AN:

3432

East Asian (EAS)

AF:

0.000791

AC:

AN:

5060

South Asian (SAS)

AF:

0.00276

AC:

AN:

4712

European-Finnish (FIN)

AF:

0.0000958

AC:

AN:

10442

Middle Eastern (MID)

AF:

0.00

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.000791

AC:

AN:

67006

Other (OTH)

AF:

0.000478

AC:

AN:

2090

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.464

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.000125

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.92

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over