chr7-135245459-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001394401.1(STRA8):c.525G>A(p.Glu175=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000574 in 716,406 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00067 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00055 ( 1 hom. )
Consequence
STRA8
NM_001394401.1 synonymous
NM_001394401.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.629
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP6
?
Variant 7-135245459-G-A is Benign according to our data. Variant chr7-135245459-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2658006.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.629 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STRA8 | NM_001394401.1 | c.525G>A | p.Glu175= | synonymous_variant | 5/9 | ENST00000662584.2 | |
STRA8 | XM_011516137.3 | c.525G>A | p.Glu175= | synonymous_variant | 4/8 | ||
STRA8 | XM_047420324.1 | c.525G>A | p.Glu175= | synonymous_variant | 5/9 | ||
STRA8 | NM_182489.3 | c.380+130G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STRA8 | ENST00000662584.2 | c.525G>A | p.Glu175= | synonymous_variant | 5/9 | NM_001394401.1 | P2 | ||
STRA8 | ENST00000275764.3 | c.446+130G>A | intron_variant | 1 | A2 | ||||
STRA8 | ENST00000667288.1 | c.380+130G>A | intron_variant | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000671 AC: 102AN: 152044Hom.: 0 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
102
AN:
152044
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:
GnomAD4 exome AF: 0.000548 AC: 309AN: 564244Hom.: 1 AF XY: 0.000527 AC XY: 162AN XY: 307124
GnomAD4 exome
AF:
AC:
309
AN:
564244
Hom.:
AF XY:
AC XY:
162
AN XY:
307124
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: 0.000670 AC: 102AN: 152162Hom.: 0 Cov.: 32 AF XY: 0.000645 AC XY: 48AN XY: 74382
GnomAD4 genome
?
AF:
AC:
102
AN:
152162
Hom.:
Cov.:
32
AF XY:
AC XY:
48
AN XY:
74382
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.:
Bravo
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2022 | STRA8: BP4, BP7 - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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