rs1363938

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000596132.5(SAXO5):​c.-17-3696T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 152,078 control chromosomes in the GnomAD database, including 1,088 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 0.11 ( 1088 hom., cov: 32)

Consequence

SAXO5
ENST00000596132.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.16
Variant links:
Genes affected
PEX11G (HGNC:20208): (peroxisomal biogenesis factor 11 gamma) The protein encoded by this gene is a member of the PEX11 family. This family is reported to regulate the number and size of peroxisomes in evolutionarily distant organisms. The protein encoded by this gene may induce clustering of peroxisomes. Alternative splicing results in multiple transcript variants that encode different protein isoforms. [provided by RefSeq, Jul 2012]
SAXO5 (HGNC:24745): (stabilizer of axonemal microtubules 5)

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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=-0.96).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PEX11GENST00000593942.5 linkuse as main transcriptc.-457+293A>G intron_variant 5 Q96HA9-2
SAXO5ENST00000596132.5 linkuse as main transcriptc.-17-3696T>C intron_variant 5

Frequencies

GnomAD3 genomes
AF:
0.108
AC:
16373
AN:
151960
Hom.:
1080
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.110
Gnomad AMI
AF:
0.0417
Gnomad AMR
AF:
0.204
Gnomad ASJ
AF:
0.0968
Gnomad EAS
AF:
0.202
Gnomad SAS
AF:
0.0929
Gnomad FIN
AF:
0.129
Gnomad MID
AF:
0.0981
Gnomad NFE
AF:
0.0769
Gnomad OTH
AF:
0.110
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.108
AC:
16400
AN:
152078
Hom.:
1088
Cov.:
32
AF XY:
0.112
AC XY:
8338
AN XY:
74366
show subpopulations
Gnomad4 AFR
AF:
0.110
Gnomad4 AMR
AF:
0.205
Gnomad4 ASJ
AF:
0.0968
Gnomad4 EAS
AF:
0.202
Gnomad4 SAS
AF:
0.0924
Gnomad4 FIN
AF:
0.129
Gnomad4 NFE
AF:
0.0769
Gnomad4 OTH
AF:
0.109
Alfa
AF:
0.0910
Hom.:
1126
Bravo
AF:
0.115
Asia WGS
AF:
0.165
AC:
573
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
0.44
DANN
Benign
0.48

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1363938; hg19: chr19-7561996; API