5-35641489-G-C

Variant summary

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

The NM_024867.4(SPEF2):ā€‹c.220G>Cā€‹(p.Gly74Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00000124 in 1,613,556 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. G74S) has been classified as Likely benign.

Frequency

Genomes: š‘“ 0.0000066 ( 0 hom., cov: 32)
Exomes š‘“: 6.8e-7 ( 0 hom. )

Consequence

SPEF2
NM_024867.4 missense

Scores

1
9
9

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.91
Variant links:
Genes affected
SPEF2 (HGNC:26293): (sperm flagellar 2) Involved in sperm axoneme assembly. Located in sperm flagellum. Implicated in spermatogenic failure 43. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

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
SPEF2NM_024867.4 linkc.220G>C p.Gly74Arg missense_variant Exon 3 of 37 ENST00000356031.8 NP_079143.3 Q9C093-1A0A140VKD0

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SPEF2ENST00000356031.8 linkc.220G>C p.Gly74Arg missense_variant Exon 3 of 37 1 NM_024867.4 ENSP00000348314.3 Q9C093-1

Frequencies

GnomAD3 genomes
AF:
0.00000658
AC:
1
AN:
151990
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000147
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
6.84e-7
AC:
1
AN:
1461566
Hom.:
0
Cov.:
33
AF XY:
0.00000138
AC XY:
1
AN XY:
727096
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:
8.99e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.00000658
AC:
1
AN:
151990
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
74214
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000147
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.53
BayesDel_addAF
Benign
-0.0085
T
BayesDel_noAF
Benign
-0.25
CADD
Uncertain
25
DANN
Pathogenic
1.0
DEOGEN2
Benign
0.094
.;.;T;T;.;.
Eigen
Uncertain
0.58
Eigen_PC
Uncertain
0.57
FATHMM_MKL
Uncertain
0.95
D
LIST_S2
Uncertain
0.89
D;D;D;D;D;D
M_CAP
Benign
0.029
D
MetaRNN
Uncertain
0.70
D;D;D;D;D;D
MetaSVM
Benign
-1.0
T
MutationAssessor
Uncertain
2.2
M;.;.;M;.;M
PrimateAI
Uncertain
0.68
T
PROVEAN
Uncertain
-3.7
D;D;.;D;D;D
REVEL
Benign
0.22
Sift
Benign
0.088
T;T;.;D;D;D
Sift4G
Benign
0.085
T;T;.;D;D;D
Polyphen
0.99
D;D;.;D;.;.
Vest4
0.68
MutPred
0.68
Gain of helix (P = 0.0225);Gain of helix (P = 0.0225);Gain of helix (P = 0.0225);Gain of helix (P = 0.0225);Gain of helix (P = 0.0225);Gain of helix (P = 0.0225);
MVP
0.37
MPC
0.25
ClinPred
0.99
D
GERP RS
5.1
Varity_R
0.43
gMVP
0.48

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.060
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: rs34307272; hg19: chr5-35641591; API