rs1363938

Variant names:

• chr19-7497110-T-C
• rs1363938
• ENST00000596132.5:c.-17-3696T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

SAXO5 (HGNC:24745): (stabilizer of axonemal microtubules 5)

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]

PEX11G Gene-Disease associations (from GenCC):

• peroxisome biogenesis disorder

  Inheritance: AR Classification: NO_KNOWN Submitted by: ClinGen

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SAXO5	ENST00000596132.5	c.-17-3696T>C		intron_variant	Intron 1 of 2	5		ENSP00000469882.1
PEX11G	ENST00000593942.5	c.-457+293A>G		intron_variant	Intron 1 of 6	5		ENSP00000472216.1

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

African (AFR) AF: 0.110 AC: 4555 AN: 41488

American (AMR) AF: 0.205 AC: 3120 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.0968 AC: 336 AN: 3472

East Asian (EAS) AF: 0.202 AC: 1046 AN: 5168

South Asian (SAS) AF: 0.0924 AC: 445 AN: 4818

European-Finnish (FIN) AF: 0.129 AC: 1370 AN: 10598

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0769 AC: 5227 AN: 67990

Other (OTH) AF: 0.109 AC: 230 AN: 2110

Alfa AF: 0.0923 Hom.: 2503

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
PhyloP100		-2.2
PromoterAI		0.011	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1363938; hg19: chr19-7561996;