rs1571228

chr9-18930224-G-Achr9-18930224-G-C

Variant summary

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

The NM_153707.4(SAXO1):c.422-1169C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.829 in 152,196 control chromosomes in the GnomAD database, including 52,357 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 0.83 (52357 hom., cov: 33)
• Consequence: SAXO1 NM_153707.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118

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=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.843 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SAXO1	NM_153707.4	c.422-1169C>T		intron_variant		ENST00000380534.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SAXO1	ENST00000380534.9	c.422-1169C>T		intron_variant		1	NM_153707.4	P3
SAXO1	ENST00000380530.1	c.219-1169C>T		intron_variant		2
SAXO1	ENST00000542071.2	c.227-1169C>T		intron_variant		3		A1
SAXO1	ENST00000649457.1	c.227-1169C>T		intron_variant				A1

Frequencies

GnomAD3 genomes AF: 0.829 AC: 126029 AN: 152078 Hom.: 52313 Cov.: 33

Gnomad AFR AF: 0.808

Gnomad AMI AF: 0.837

Gnomad AMR AF: 0.851

Gnomad ASJ AF: 0.835

Gnomad EAS AF: 0.700

Gnomad SAS AF: 0.787

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.849

Gnomad OTH AF: 0.835

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

GnomAD4 genome AF: 0.829 AC: 126133 AN: 152196 Hom.: 52357 Cov.: 33 AF XY: 0.827 AC XY: 61525 AN XY: 74400

Gnomad4 AFR AF: 0.808

Gnomad4 AMR AF: 0.851

Gnomad4 ASJ AF: 0.835

Gnomad4 EAS AF: 0.701

Gnomad4 SAS AF: 0.786

Gnomad4 FIN AF: 0.821

Gnomad4 NFE AF: 0.849

Gnomad4 OTH AF: 0.835

Alfa AF: 0.831 Hom.: 11038

Bravo AF: 0.830

Asia WGS AF: 0.758 AC: 2634 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.5
Dann	Benign	0.20

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: rs1571228; hg19: chr9-18930222; COSMIC: COSV65871746;