dbSNP rs199601443: CATSPERD:p.Arg164His (chr19-5739357-G-A) – ACMG Classification: Likely_benign (-6 pts)

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate

The NM_152784.4(CATSPERD):c.491G>A(p.Arg164His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000138 in 1,577,942 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R164C) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.00023 ( 0 hom., cov: 31)

Exomes 𝑓: 0.00013 ( 0 hom. )

Consequence

CATSPERD
NM_152784.4 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -3.49

Publications

0 publications found

Variant links:

Genes affected

CATSPERD (HGNC:28598): (cation channel sperm associated auxiliary subunit delta) Predicted to be involved in flagellated sperm motility and sperm capacitation. Predicted to be located in sperm principal piece. Predicted to be part of CatSper complex. [provided by Alliance of Genome Resources, Apr 2022]

CATSPERD links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -6 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.017644405).

BP6

Variant 19-5739357-G-A is Benign according to our data. Variant chr19-5739357-G-A is described in ClinVar as Likely_benign. ClinVar VariationId is 2393570.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152784.4. 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
	CATSPERD	NM_152784.4	MANE Select	c.491G>A	p.Arg164His	missense	Exon 7 of 22	NP_689997.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CATSPERD	ENST00000381624.4	TSL:1 MANE Select	c.491G>A	p.Arg164His	missense	Exon 7 of 22	ENSP00000371037.3	Q86XM0-1

Frequencies

GnomAD3 genomes

AF:

0.000234

AC:

AN:

149314

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000149

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000741

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000195

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000237

Gnomad OTH

AF:

0.000491

GnomAD2 exomes

AF:

0.000153

AC:

AN:

229364

AF XY:

0.000152

show subpopulations

Gnomad AFR exome

AF:

0.000134

Gnomad AMR exome

AF:

0.000136

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.000923

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000121

Gnomad OTH exome

AF:

0.000178

GnomAD4 exome

AF:

0.000128

AC:

183

AN:

1428628

Hom.:

Cov.:

AF XY:

0.000125

AC XY:

AN XY:

711344

show subpopulations

African (AFR)

AF:

0.0000636

AC:

AN:

31458

American (AMR)

AF:

0.000155

AC:

AN:

38770

Ashkenazi Jewish (ASJ)

AF:

0.0000388

AC:

AN:

25742

East Asian (EAS)

AF:

0.000279

AC:

AN:

39434

South Asian (SAS)

AF:

0.0000370

AC:

AN:

81026

European-Finnish (FIN)

AF:

0.0000194

AC:

AN:

51652

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5594

European-Non Finnish (NFE)

AF:

0.000140

AC:

153

AN:

1095838

Other (OTH)

AF:

0.000101

AC:

AN:

59114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.437

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:

0.000234

AC:

AN:

149314

Hom.:

Cov.:

AF XY:

0.000193

AC XY:

AN XY:

72564

show subpopulations

African (AFR)

AF:

0.000149

AC:

AN:

40312

American (AMR)

AF:

0.000741

AC:

AN:

14836

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3456

East Asian (EAS)

AF:

0.000195

AC:

AN:

5132

South Asian (SAS)

AF:

0.00

AC:

AN:

4750

European-Finnish (FIN)

AF:

0.00

AC:

AN:

9944

Middle Eastern (MID)

AF:

0.00

AC:

AN:

314

European-Non Finnish (NFE)

AF:

0.000237

AC:

AN:

67626

Other (OTH)

AF:

0.000491

AC:

AN:

2036

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

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:

0.000255

Hom.:

Bravo

AF:

0.000246

ExAC

AF:

0.000166

AC:

EpiCase

AF:

0.000164

EpiControl

AF:

0.000416

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.086

BayesDel_addAF

Benign

-0.67

BayesDel_noAF

Benign

-0.81

CADD

Benign

0.0010

(source)

DANN

Benign

0.92

DEOGEN2

Benign

0.0024

Eigen

Benign

-1.9

Eigen_PC

Benign

-2.0

FATHMM_MKL

Benign

0.0022

LIST_S2

Benign

0.53

M_CAP

Benign

0.0015

MetaRNN

Benign

0.018

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.20

PhyloP100

-3.5

PrimateAI

Benign

0.22

PROVEAN

Benign

-1.0

REVEL

Benign

0.0030

Sift

Benign

0.32

Sift4G

Benign

0.39

Polyphen

0.059

Vest4

0.074

MVP

0.030

MPC

0.20

ClinPred

0.0097

GERP RS

-6.2

Varity_R

0.026

gMVP

0.16

Mutation Taster

=300/0

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.15

Details are displayed if max score is > 0.2

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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