9-18930882-T-G

Position:

• chr9-18930882-T-G

Variant summary

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

The NM_153707.4(SAXO1):​c.422-1827A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.809 in 152,116 control chromosomes in the GnomAD database, including 50,023 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 0.81 (50023 hom., cov: 32)
• Consequence: SAXO1 NM_153707.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.217

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=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.843 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SAXO1	NM_153707.4	c.422-1827A>C		intron_variant		ENST00000380534.9	NP_714918.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SAXO1	ENST00000380534.9	c.422-1827A>C		intron_variant		1	NM_153707.4	ENSP00000369907	P3
SAXO1	ENST00000380530.1	c.219-1827A>C		intron_variant		2		ENSP00000369902
SAXO1	ENST00000542071.2	c.227-1827A>C		intron_variant		3		ENSP00000438823	A1
SAXO1	ENST00000649457.1	c.227-1827A>C		intron_variant				ENSP00000497677	A1

Frequencies

GnomAD3 genomes AF: 0.809 AC: 122929 AN: 151996 Hom.: 49989 Cov.: 32

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.838

Gnomad AMR AF: 0.841

Gnomad ASJ AF: 0.830

Gnomad EAS AF: 0.702

Gnomad SAS AF: 0.840

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.849

Gnomad OTH AF: 0.818

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

GnomAD4 genome AF: 0.809 AC: 123019 AN: 152116 Hom.: 50023 Cov.: 32 AF XY: 0.808 AC XY: 60124 AN XY: 74366

Gnomad4 AFR AF: 0.734

Gnomad4 AMR AF: 0.842

Gnomad4 ASJ AF: 0.830

Gnomad4 EAS AF: 0.702

Gnomad4 SAS AF: 0.839

Gnomad4 FIN AF: 0.821

Gnomad4 NFE AF: 0.849

Gnomad4 OTH AF: 0.819

Alfa AF: 0.841 Hom.: 106625

Bravo AF: 0.805

Asia WGS AF: 0.774 AC: 2688 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	0.97
DANN	Benign	0.38

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: rs4977469; hg19: chr9-18930880; COSMIC: COSV65871756;