chr14-88385821-G-C
Variant names:
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PVS1_StrongPS1_ModeratePM2
The NM_018418.5(SPATA7):āc.3G>Cā(p.Met1?) variant causes a start lost change. The variant allele was found at a frequency of 0.00000249 in 1,606,674 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: š 0.000013 ( 0 hom., cov: 34)
Exomes š: 0.0000014 ( 0 hom. )
Consequence
SPATA7
NM_018418.5 start_lost
NM_018418.5 start_lost
Scores
5
5
6
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.71
Genes affected
SPATA7 (HGNC:20423): (spermatogenesis associated 7) This gene, originally isolated from testis, is also expressed in retina. Mutations in this gene are associated with Leber congenital amaurosis and juvenile retinitis pigmentosa. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2010]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
PVS1
Start lost variant, next in-frame start position is after 5 pathogenic variants. Next in-frame start position is after 153 CDS bases. Genomic position: 88393451. Lost 0.085 part of the original CDS.
PS1
Another start lost variant in NM_018418.5 (SPATA7) was described as [Pathogenic] in Lovd
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152216Hom.: 0 Cov.: 34
GnomAD3 genomes
AF:
AC:
2
AN:
152216
Hom.:
Cov.:
34
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.00000428 AC: 1AN: 233902Hom.: 0 AF XY: 0.00000789 AC XY: 1AN XY: 126780
GnomAD3 exomes
AF:
AC:
1
AN:
233902
Hom.:
AF XY:
AC XY:
1
AN XY:
126780
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00000138 AC: 2AN: 1454458Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 722734
GnomAD4 exome
AF:
AC:
2
AN:
1454458
Hom.:
Cov.:
31
AF XY:
AC XY:
1
AN XY:
722734
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152216Hom.: 0 Cov.: 34 AF XY: 0.0000269 AC XY: 2AN XY: 74366
GnomAD4 genome
AF:
AC:
2
AN:
152216
Hom.:
Cov.:
34
AF XY:
AC XY:
2
AN XY:
74366
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
ExAC
AF:
AC:
1
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
.;T;.;T;T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
.;D;D;D;D;D
M_CAP
Pathogenic
D
MetaRNN
Pathogenic
D;D;D;D;D;D
MetaSVM
Benign
T
PROVEAN
Benign
N;N;N;N;N;N
REVEL
Benign
Sift
Pathogenic
D;D;D;D;D;D
Sift4G
Benign
T;T;T;.;T;T
Polyphen
D;B;D;.;.;.
Vest4
MutPred
Loss of methylation at R6 (P = 0.066);Loss of methylation at R6 (P = 0.066);Loss of methylation at R6 (P = 0.066);Loss of methylation at R6 (P = 0.066);Loss of methylation at R6 (P = 0.066);Loss of methylation at R6 (P = 0.066);
MVP
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at