rs1363938

Positions:

• chr19-7497110-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.16

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)

ACMG classification

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
PEX11G	ENST00000593942.5	c.-457+293A>G		intron_variant		5
SAXO5	ENST00000596132.5	c.-17-3696T>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16373 AN: 151960 Hom.: 1080 Cov.: 32

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

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

Other links and lift over

dbSNP: rs1363938; hg19: chr19-7561996;