chr19-5744490-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_152784.4(CATSPERD):​c.637C>T​(p.Leu213Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000616 in 1,460,014 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L213V) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000062 ( 0 hom. )

Consequence

CATSPERD
NM_152784.4 missense

Scores

1
6
12

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.99
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]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CATSPERDNM_152784.4 linkc.637C>T p.Leu213Phe missense_variant Exon 8 of 22 ENST00000381624.4 NP_689997.3 Q86XM0-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CATSPERDENST00000381624.4 linkc.637C>T p.Leu213Phe missense_variant Exon 8 of 22 1 NM_152784.4 ENSP00000371037.3 Q86XM0-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
0.00000616
AC:
9
AN:
1460014
Hom.:
0
Cov.:
30
AF XY:
0.00000413
AC XY:
3
AN XY:
726302
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000810
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32
TwinsUK
AF:
0.000270
AC:
1
ALSPAC
AF:
0.000259
AC:
1
EpiCase
AF:
0.00
EpiControl
AF:
0.0000593

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.47
BayesDel_addAF
Benign
-0.13
T
BayesDel_noAF
Benign
-0.42
CADD
Benign
21
DANN
Uncertain
1.0
DEOGEN2
Benign
0.028
T
Eigen
Benign
0.086
Eigen_PC
Benign
-0.11
FATHMM_MKL
Benign
0.46
N
LIST_S2
Benign
0.39
T
M_CAP
Benign
0.029
D
MetaRNN
Uncertain
0.71
D
MetaSVM
Benign
-0.81
T
MutationAssessor
Uncertain
2.1
M
PrimateAI
Benign
0.48
T
PROVEAN
Uncertain
-3.0
D
REVEL
Benign
0.15
Sift
Uncertain
0.017
D
Sift4G
Pathogenic
0.0
D
Polyphen
1.0
D
Vest4
0.58
MVP
0.38
MPC
0.70
ClinPred
0.76
D
GERP RS
2.6
Varity_R
0.20
gMVP
0.64

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.040
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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs540346018; hg19: chr19-5744501; API