Genetic Variant NM_001039496.2:c.*206_*207insAGTGACCTTCATTCGGTCACCGCAGTGACCTTCATTCGGTCACCGC (chr11-64304830-C-CGTGACCTTCATTCGGTCACCGCAGTGACCTTCATTCGGTCACCGCA) – 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.*184_*185insGTGACCTTCATTCGGTCACCGCAGTGACCTTCATTCGGTCACCGCA variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000345 in 544,834 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 INS_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 ( 1 hom., cov: 32)

Exomes 𝑓: 0.000086 ( 0 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:

ESRRA (HGNC:3471): (estrogen related receptor alpha) The protein encoded by this gene is a nuclear receptor that is most closely related to the estrogen receptor. This protein acts as a site-specific transcription factor and interacts with members of the PGC-1 family of transcription cofactors to regulate the expression of most genes involved in cellular energy production as well as in the process of mitochondrial biogenesis. A processed pseudogene of ESRRA is located on chromosome 13q12.1. [provided by RefSeq, Jun 2019]

ESRRA links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001039496.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CATSPERZ	NM_001039496.2	MANE Select	c.184_185insGTGACCTTCATTCGGTCACCGCAGTGACCTTCATTCGGTCACCGCA		downstream_gene	N/A	NP_001034585.1	Q9NTU4
	KCNK4-CATSPERZ	NR_133662.1		n.61_62insGTGACCTTCATTCGGTCACCGCAGTGACCTTCATTCGGTCACCGCA		downstream_gene	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CATSPERZ	ENST00000328404.8	TSL:1 MANE Select	c.184_185insGTGACCTTCATTCGGTCACCGCAGTGACCTTCATTCGGTCACCGCA	downstream_gene	N/A	ENSP00000491717.1	Q9NTU4
KCNK4-CATSPERZ	ENST00000539086.5	TSL:1	n.61_62insGTGACCTTCATTCGGTCACCGCAGTGACCTTCATTCGGTCACCGCA	downstream_gene	N/A
ESRRA	ENST00000965463.1		c.-344_-343insGTGACCTTCATTCGGTCACCGCAGTGACCTTCATTCGGTCACCGCA	upstream_gene	N/A	ENSP00000635522.1

Frequencies

GnomAD3 genomes

AF:

0.00103

AC:

154

AN:

150064

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000586

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000528

Gnomad ASJ

AF:

0.000583

Gnomad EAS

AF:

0.000591

Gnomad SAS

AF:

0.000212

Gnomad FIN

AF:

0.000479

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00161

Gnomad OTH

AF:

0.00145

GnomAD4 exome

AF:

0.0000862

AC:

AN:

394654

Hom.:

AF XY:

0.0000722

AC XY:

AN XY:

207804

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

11380

American (AMR)

AF:

0.0000639

AC:

AN:

15642

Ashkenazi Jewish (ASJ)

AF:

0.0000846

AC:

AN:

11824

East Asian (EAS)

AF:

0.0000371

AC:

AN:

26970

South Asian (SAS)

AF:

0.00

AC:

AN:

38606

European-Finnish (FIN)

AF:

0.0000771

AC:

AN:

25926

Middle Eastern (MID)

AF:

0.000534

AC:

AN:

1872

European-Non Finnish (NFE)

AF:

0.0000961

AC:

AN:

239422

Other (OTH)

AF:

0.000217

AC:

AN:

23012

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.566

Heterozygous variant carriers

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:

154

AN:

150180

Hom.:

Cov.:

AF XY:

0.000981

AC XY:

AN XY:

73364

show subpopulations

African (AFR)

AF:

0.000584

AC:

AN:

41088

American (AMR)

AF:

0.000527

AC:

AN:

15170

Ashkenazi Jewish (ASJ)

AF:

0.000583

AC:

AN:

3432

East Asian (EAS)

AF:

0.000593

AC:

AN:

5060

South Asian (SAS)

AF:

0.000212

AC:

AN:

4712

European-Finnish (FIN)

AF:

0.000479

AC:

AN:

10442

Middle Eastern (MID)

AF:

0.00

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.00161

AC:

108

AN:

67002

Other (OTH)

AF:

0.00144

AC:

AN:

2090

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

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:

0.0000625

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.92

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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NM_001039496.2:c.206_207insAGTGACCTTCATTCGGTCACCGCAGTGACCTTCATTCGGTCACCGC

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over