chr11-64300838-C-T

Position:

• chr11-64300838-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001039496.2(CATSPERZ):​c.203C>T​(p.Pro68Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 1,559,112 control chromosomes in the GnomAD database, including 17,728 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

• Frequency:
  • Genomes: 𝑓 0.12 (1354 hom., cov: 33)
  • Exomes 𝑓: 0.15 (16374 hom.)
• Consequence: CATSPERZ NM_001039496.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.84

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]

KCNK4-CATSPERZ (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.0045560896).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CATSPERZ	NM_001039496.2	c.203C>T	p.Pro68Leu	missense_variant	2/5	ENST00000328404.8
KCNK4-CATSPERZ	NR_133662.1	n.2210C>T		non_coding_transcript_exon_variant	8/11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CATSPERZ	ENST00000328404.8	c.203C>T	p.Pro68Leu	missense_variant	2/5	1	NM_001039496.2	P2
CATSPERZ	ENST00000539943.1	c.77C>T	p.Pro26Leu	missense_variant	1/4	2		A2

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18033 AN: 152122 Hom.: 1355 Cov.: 33

Gnomad AFR AF: 0.0427

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.0710

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.146

GnomAD3 exomes AF: 0.130 AC: 21111 AN: 162324 Hom.: 1514 AF XY: 0.131 AC XY: 11486 AN XY: 87520

Gnomad AFR exome AF: 0.0393

Gnomad AMR exome AF: 0.108

Gnomad ASJ exome AF: 0.112

Gnomad EAS exome AF: 0.114

Gnomad SAS exome AF: 0.0847

Gnomad FIN exome AF: 0.160

Gnomad NFE exome AF: 0.163

Gnomad OTH exome AF: 0.147

GnomAD4 exome AF: 0.149 AC: 209996 AN: 1406872 Hom.: 16374 Cov.: 33 AF XY: 0.148 AC XY: 103094 AN XY: 694946

Gnomad4 AFR exome AF: 0.0371

Gnomad4 AMR exome AF: 0.108

Gnomad4 ASJ exome AF: 0.113

Gnomad4 EAS exome AF: 0.106

Gnomad4 SAS exome AF: 0.0826

Gnomad4 FIN exome AF: 0.160

Gnomad4 NFE exome AF: 0.160

Gnomad4 OTH exome AF: 0.151

GnomAD4 genome AF: 0.118 AC: 18037 AN: 152240 Hom.: 1354 Cov.: 33 AF XY: 0.119 AC XY: 8824 AN XY: 74428

Gnomad4 AFR AF: 0.0426

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.112

Gnomad4 SAS AF: 0.0714

Gnomad4 FIN AF: 0.166

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.151

Alfa AF: 0.150 Hom.: 3450

Bravo AF: 0.113

TwinsUK AF: 0.157 AC: 582

ALSPAC AF: 0.157 AC: 606

ESP6500AA AF: 0.0430 AC: 167

ESP6500EA AF: 0.143 AC: 1167

ExAC AF: 0.0883 AC: 9737

Asia WGS AF: 0.115 AC: 398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.086
BayesDel_addAF	Benign	-0.82	T
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.056
DANN	Benign	0.81
DEOGEN2	Benign	0.011	T;.
Eigen	Benign	-1.6
Eigen_PC	Benign	-1.7
FATHMM_MKL	Benign	0.011	N
LIST_S2	Benign	0.46	T;T
MetaRNN	Benign	0.0046	T;T
MetaSVM	Benign	-1.0	T
MutationTaster	Benign	1.0	P;P
PrimateAI	Benign	0.22	T
PROVEAN	Benign	-1.2	.;N
REVEL	Benign	0.014
Sift	Benign	0.28	.;T
Sift4G	Benign	0.091	.;T
Polyphen		0.0020	B;.
Vest4		0.014
MPC		0.50
ClinPred		0.0034	T
GERP RS		-6.6
Varity_R		0.025
gMVP		0.021

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: rs2286614; hg19: chr11-64068310;