rs2793483
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001166271.3(SPATA13):c.-112+24617G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.642 in 152,026 control chromosomes in the GnomAD database, including 31,373 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 0.64 ( 31373 hom., cov: 32)
Consequence
SPATA13
NM_001166271.3 intron
NM_001166271.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.11
Genes affected
SPATA13 (HGNC:23222): (spermatogenesis associated 13) Enables guanyl-nucleotide exchange factor activity and identical protein binding activity. Involved in cell migration; plasma membrane bounded cell projection assembly; and regulation of cell migration. Located in several cellular components, including filopodium; lamellipodium; and ruffle membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.65 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPATA13 | NM_001166271.3 | c.-112+24617G>A | intron_variant | ENST00000382108.8 | |||
SPATA13 | NM_001286792.2 | c.76-37270G>A | intron_variant | ||||
SPATA13 | NM_153023.4 | c.-223+24617G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPATA13 | ENST00000382108.8 | c.-112+24617G>A | intron_variant | 5 | NM_001166271.3 | ||||
SPATA13 | ENST00000424834.6 | c.-111-37270G>A | intron_variant | 1 | |||||
SPATA13 | ENST00000382095.8 | c.-223+24617G>A | intron_variant | 2 | |||||
SPATA13 | ENST00000466831.2 | n.211+24617G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.642 AC: 97469AN: 151908Hom.: 31338 Cov.: 32
GnomAD3 genomes
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.642 AC: 97547AN: 152026Hom.: 31373 Cov.: 32 AF XY: 0.639 AC XY: 47463AN XY: 74312
GnomAD4 genome
?
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32
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47463
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74312
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2282
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3472
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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