rs10511666

chr9-18969424-A-C

Variant summary

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

The NM_153707.4(SAXO1):c.39-18487T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 152,104 control chromosomes in the GnomAD database, including 6,990 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 0.20 (6990 hom., cov: 32)
• Consequence: SAXO1 NM_153707.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.286

Genes affected

SAXO1 (HGNC:28566): (stabilizer of axonemal microtubules 1) Enables microtubule binding activity. Involved in several processes, including cold acclimation; positive regulation of cilium assembly; and protein stabilization. Located in microtubule cytoskeleton and sperm flagellum. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SAXO1	NM_153707.4	c.39-18487T>G		intron_variant		ENST00000380534.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SAXO1	ENST00000380534.9	c.39-18487T>G		intron_variant		1	NM_153707.4	P3

Frequencies

GnomAD3 genomes AF: 0.204 AC: 30987 AN: 151988 Hom.: 6966 Cov.: 32

Gnomad AFR AF: 0.564

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0896

Gnomad ASJ AF: 0.0524

Gnomad EAS AF: 0.0887

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.0864

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0541

Gnomad OTH AF: 0.169

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.204 AC: 31056 AN: 152104 Hom.: 6990 Cov.: 32 AF XY: 0.201 AC XY: 14930 AN XY: 74358

Gnomad4 AFR AF: 0.565

Gnomad4 AMR AF: 0.0895

Gnomad4 ASJ AF: 0.0524

Gnomad4 EAS AF: 0.0885

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.0864

Gnomad4 NFE AF: 0.0542

Gnomad4 OTH AF: 0.169

Alfa AF: 0.0810 Hom.: 1326

Bravo AF: 0.220

Asia WGS AF: 0.132 AC: 459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
Cadd	Benign	14
Dann	Benign	0.53

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10511666; hg19: chr9-18969422;