rs10123624

Positions:

• chr9-19025387-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_153707.4(SAXO1):​c.38+7484C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.486 in 151,758 control chromosomes in the GnomAD database, including 19,787 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 0.49 (19787 hom., cov: 32)
• Consequence: SAXO1 NM_153707.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.49

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.722 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SAXO1	NM_153707.4	c.38+7484C>A		intron_variant		ENST00000380534.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SAXO1	ENST00000380534.9	c.38+7484C>A		intron_variant		1	NM_153707.4	P3

Frequencies

GnomAD3 genomes AF: 0.486 AC: 73631 AN: 151638 Hom.: 19749 Cov.: 32

Gnomad AFR AF: 0.729

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.486 AC: 73734 AN: 151758 Hom.: 19787 Cov.: 32 AF XY: 0.480 AC XY: 35555 AN XY: 74150

Gnomad4 AFR AF: 0.729

Gnomad4 AMR AF: 0.367

Gnomad4 ASJ AF: 0.397

Gnomad4 EAS AF: 0.173

Gnomad4 SAS AF: 0.404

Gnomad4 FIN AF: 0.396

Gnomad4 NFE AF: 0.414

Gnomad4 OTH AF: 0.472

Alfa AF: 0.454 Hom.: 2258

Bravo AF: 0.496

Asia WGS AF: 0.320 AC: 1112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
CADD	Benign	18
DANN	Benign	0.73

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: rs10123624; hg19: chr9-19025385;