13-24222869-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001166271.3(SPATA13):c.-61C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000721 in 1,543,084 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0035 ( 3 hom., cov: 33)
Exomes 𝑓: 0.00041 ( 1 hom. )
Consequence
SPATA13
NM_001166271.3 5_prime_UTR
NM_001166271.3 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.46
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
?
Variant 13-24222869-C-T is Benign according to our data. Variant chr13-24222869-C-T is described in ClinVar as [Benign]. Clinvar id is 3038489.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAd at 534 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPATA13 | NM_001166271.3 | c.-61C>T | 5_prime_UTR_variant | 2/13 | ENST00000382108.8 | ||
SPATA13 | NM_001286792.2 | c.126C>T | p.Asp42= | synonymous_variant | 4/15 | ||
SPATA13 | NM_153023.4 | c.-222-26608C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPATA13 | ENST00000382108.8 | c.-61C>T | 5_prime_UTR_variant | 2/13 | 5 | NM_001166271.3 | |||
SPATA13 | ENST00000424834.6 | c.-61C>T | 5_prime_UTR_variant | 4/15 | 1 | ||||
SPATA13 | ENST00000382095.8 | c.-222-26608C>T | intron_variant | 2 | |||||
SPATA13 | ENST00000466831.2 | n.262C>T | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00351 AC: 534AN: 152104Hom.: 3 Cov.: 33
GnomAD3 genomes
?
AF:
AC:
534
AN:
152104
Hom.:
Cov.:
33
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:
GnomAD3 exomes AF: 0.000787 AC: 116AN: 147424Hom.: 0 AF XY: 0.000698 AC XY: 55AN XY: 78836
GnomAD3 exomes
AF:
AC:
116
AN:
147424
Hom.:
AF XY:
AC XY:
55
AN XY:
78836
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000414 AC: 576AN: 1390862Hom.: 1 Cov.: 29 AF XY: 0.000368 AC XY: 252AN XY: 684712
GnomAD4 exome
AF:
AC:
576
AN:
1390862
Hom.:
Cov.:
29
AF XY:
AC XY:
252
AN XY:
684712
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: 0.00352 AC: 536AN: 152222Hom.: 3 Cov.: 33 AF XY: 0.00351 AC XY: 261AN XY: 74434
GnomAD4 genome
?
AF:
AC:
536
AN:
152222
Hom.:
Cov.:
33
AF XY:
AC XY:
261
AN XY:
74434
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:
Asia WGS
AF:
AC:
5
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
SPATA13-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 22, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
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