rs112976233
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BS1BS2
The NM_018418.5(SPATA7):āc.1255T>Cā(p.Leu419=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00268 in 1,608,652 control chromosomes in the GnomAD database, including 95 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: š 0.014 ( 51 hom., cov: 32)
Exomes š: 0.0015 ( 44 hom. )
Consequence
SPATA7
NM_018418.5 synonymous
NM_018418.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.03
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.64).
BP6
?
Variant 14-88437877-T-C is Benign according to our data. Variant chr14-88437877-T-C is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 534952.We mark this variant Likely_benign, oryginal submissions are: {Benign=2, Uncertain_significance=1}. Variant chr14-88437877-T-C is described in Lovd as [Likely_benign].
BP7
?
Synonymous conserved (PhyloP=2.03 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0143 (2170/152268) while in subpopulation AFR AF= 0.0488 (2027/41542). AF 95% confidence interval is 0.047. There are 51 homozygotes in gnomad4. There are 1032 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 51 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPATA7 | NM_018418.5 | c.1255T>C | p.Leu419= | synonymous_variant | 12/12 | ENST00000393545.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPATA7 | ENST00000393545.9 | c.1255T>C | p.Leu419= | synonymous_variant | 12/12 | 1 | NM_018418.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0142 AC: 2157AN: 152150Hom.: 50 Cov.: 32
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GnomAD3 exomes AF: 0.00367 AC: 908AN: 247576Hom.: 12 AF XY: 0.00281 AC XY: 376AN XY: 133708
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GnomAD4 exome AF: 0.00148 AC: 2149AN: 1456384Hom.: 44 Cov.: 32 AF XY: 0.00133 AC XY: 966AN XY: 723854
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GnomAD4 genome ? AF: 0.0143 AC: 2170AN: 152268Hom.: 51 Cov.: 32 AF XY: 0.0139 AC XY: 1032AN XY: 74444
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:2
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
Leber congenital amaurosis 3 Benign:2
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 28, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 26, 2024 | - - |
Retinitis pigmentosa Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 28, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. - |
Computational scores
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Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at