GeneBe

NM_018418.5:c.19+102delG

Variant names:

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_018418.5(SPATA7):​c.19+102delG variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 1.0 ( 76132 hom., cov: 0)
Exomes 𝑓: 1.0 ( 695390 hom. )

Consequence

SPATA7
NM_018418.5 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.182

Publications

4 publications found
Variant links:
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]
SPATA7 Gene-Disease associations (from GenCC):
  • Leber congenital amaurosis 3
    Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics
  • Leber congenital amaurosis
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
  • retinitis pigmentosa
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
  • severe early-childhood-onset retinal dystrophy
    Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP6
Variant 14-88385935-TG-T is Benign according to our data. Variant chr14-88385935-TG-T is described in ClinVar as [Benign]. Clinvar id is 801397.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.994 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SPATA7NM_018418.5 linkc.19+102delG intron_variant Intron 1 of 11 ENST00000393545.9 NP_060888.2 Q9P0W8-1V9HVY9

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SPATA7ENST00000393545.9 linkc.19+102delG intron_variant Intron 1 of 11 1 NM_018418.5 ENSP00000377176.4 Q9P0W8-1

Frequencies

GnomAD3 genomes
AF:
1.00
AC:
152148
AN:
152150
Hom.:
76073
Cov.:
0
show subpopulations
Gnomad AFR
AF:
1.00
Gnomad AMI
AF:
1.00
Gnomad AMR
AF:
1.00
Gnomad ASJ
AF:
1.00
Gnomad EAS
AF:
1.00
Gnomad SAS
AF:
1.00
Gnomad FIN
AF:
1.00
Gnomad MID
AF:
1.00
Gnomad NFE
AF:
1.00
Gnomad OTH
AF:
1.00
GnomAD2 exomes
AF:
1.00
AC:
144256
AN:
144256
AF XY:
1.00
show subpopulations
Gnomad AFR exome
AF:
1.00
Gnomad AMR exome
AF:
1.00
Gnomad ASJ exome
AF:
1.00
Gnomad EAS exome
AF:
1.00
Gnomad FIN exome
AF:
1.00
Gnomad NFE exome
AF:
1.00
Gnomad OTH exome
AF:
1.00
GnomAD4 exome
AF:
1.00
AC:
1390788
AN:
1390796
Hom.:
695390
Cov.:
0
AF XY:
1.00
AC XY:
685832
AN XY:
685836
show subpopulations
African (AFR)
AF:
1.00
AC:
31686
AN:
31686
American (AMR)
AF:
1.00
AC:
35628
AN:
35628
Ashkenazi Jewish (ASJ)
AF:
1.00
AC:
25106
AN:
25106
East Asian (EAS)
AF:
1.00
AC:
35920
AN:
35920
South Asian (SAS)
AF:
1.00
AC:
79116
AN:
79116
European-Finnish (FIN)
AF:
1.00
AC:
43274
AN:
43274
Middle Eastern (MID)
AF:
1.00
AC:
4604
AN:
4604
European-Non Finnish (NFE)
AF:
1.00
AC:
1077762
AN:
1077770
Other (OTH)
AF:
1.00
AC:
57692
AN:
57692
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.481
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
21296
42592
63888
85184
106480
<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:
1.00
AC:
152266
AN:
152268
Hom.:
76132
Cov.:
0
AF XY:
1.00
AC XY:
74436
AN XY:
74436
show subpopulations
African (AFR)
AF:
1.00
AC:
41576
AN:
41576
American (AMR)
AF:
1.00
AC:
15308
AN:
15308
Ashkenazi Jewish (ASJ)
AF:
1.00
AC:
3472
AN:
3472
East Asian (EAS)
AF:
1.00
AC:
5112
AN:
5112
South Asian (SAS)
AF:
1.00
AC:
4826
AN:
4826
European-Finnish (FIN)
AF:
1.00
AC:
10622
AN:
10622
Middle Eastern (MID)
AF:
1.00
AC:
294
AN:
294
European-Non Finnish (NFE)
AF:
1.00
AC:
68028
AN:
68030
Other (OTH)
AF:
1.00
AC:
2116
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.650
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
914
1828
2742
3656
4570
<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:
1.00
Hom.:
13752
Bravo
AF:
1.00
Asia WGS
AF:
1.00
AC:
3478
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
May 28, 2019
Mendelics
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.18
Mutation Taster
=100/0
polymorphism (auto)

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

Other links and lift over

dbSNP: rs5810413; hg19: chr14-88852279; COSMIC: COSV50419195; API