7-135249016-C-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001394401.1(STRA8):c.879+2314C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 152,068 control chromosomes in the GnomAD database, including 5,582 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.25 ( 5582 hom., cov: 32)
Consequence
STRA8
NM_001394401.1 intron
NM_001394401.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.171
Publications
3 publications found
Genes affected
STRA8 (HGNC:30653): (stimulated by retinoic acid 8) This gene encodes a retinoic acid-responsive protein. A homologous protein in mouse has been shown to be involved in the regulation of meiotic initiation in both spermatogenesis and oogenesis, though feature differences between the mouse and human proteins suggest that these homologs are not entirely functionally equivalent. It is thought that this gene may play a role in spermatogenesis in humans. [provided by RefSeq, Nov 2010]
STRA8 Gene-Disease associations (from GenCC):
- male infertility with azoospermia or oligozoospermia due to single gene mutationInheritance: AR Classification: MODERATE Submitted by: King Faisal Specialist Hospital and Research Center
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
STRA8 | NM_001394401.1 | c.879+2314C>A | intron_variant | Intron 6 of 8 | ENST00000662584.2 | NP_001381330.1 | ||
STRA8 | NM_182489.3 | c.666+2314C>A | intron_variant | Intron 6 of 8 | NP_872295.2 | |||
STRA8 | XM_011516137.3 | c.879+2314C>A | intron_variant | Intron 5 of 7 | XP_011514439.1 | |||
STRA8 | XM_047420324.1 | c.879+2314C>A | intron_variant | Intron 6 of 8 | XP_047276280.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
STRA8 | ENST00000662584.2 | c.879+2314C>A | intron_variant | Intron 6 of 8 | NM_001394401.1 | ENSP00000499386.1 | ||||
STRA8 | ENST00000275764.3 | c.732+2314C>A | intron_variant | Intron 6 of 8 | 1 | ENSP00000275764.3 | ||||
STRA8 | ENST00000667288.1 | c.666+2314C>A | intron_variant | Intron 6 of 8 | ENSP00000499721.1 | |||||
ENSG00000290805 | ENST00000637483.1 | n.404-1799G>T | intron_variant | Intron 3 of 4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.246 AC: 37415AN: 151950Hom.: 5585 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
37415
AN:
151950
Hom.:
Cov.:
32
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.246 AC: 37408AN: 152068Hom.: 5582 Cov.: 32 AF XY: 0.249 AC XY: 18515AN XY: 74292 show subpopulations
GnomAD4 genome
AF:
AC:
37408
AN:
152068
Hom.:
Cov.:
32
AF XY:
AC XY:
18515
AN XY:
74292
show subpopulations
African (AFR)
AF:
AC:
3622
AN:
41516
American (AMR)
AF:
AC:
4570
AN:
15278
Ashkenazi Jewish (ASJ)
AF:
AC:
609
AN:
3470
East Asian (EAS)
AF:
AC:
2906
AN:
5156
South Asian (SAS)
AF:
AC:
1162
AN:
4810
European-Finnish (FIN)
AF:
AC:
3291
AN:
10548
Middle Eastern (MID)
AF:
AC:
37
AN:
294
European-Non Finnish (NFE)
AF:
AC:
20371
AN:
67970
Other (OTH)
AF:
AC:
546
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1347
2694
4040
5387
6734
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
384
768
1152
1536
1920
<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:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1312
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
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
Publications
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