9-19022472-C-T

Variant names:

• chr9-19022472-C-T
• rs10511668
• NM_153707.4:c.38+10399G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_153707.4(SAXO1):​c.38+10399G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 152,054 control chromosomes in the GnomAD database, including 10,597 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 0.35 (10597 hom., cov: 33)
• Consequence: SAXO1 NM_153707.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.420
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SAXO1	NM_153707.4	c.38+10399G>A		intron_variant	Intron 1 of 3	ENST00000380534.9	NP_714918.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SAXO1	ENST00000380534.9	c.38+10399G>A		intron_variant	Intron 1 of 3	1	NM_153707.4	ENSP00000369907.4

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53194 AN: 151936 Hom.: 10607 Cov.: 33

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.350 AC: 53190 AN: 152054 Hom.: 10597 Cov.: 33 AF XY: 0.351 AC XY: 26063 AN XY: 74318

African (AFR) AF: 0.142 AC: 5909 AN: 41492

American (AMR) AF: 0.405 AC: 6187 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.469 AC: 1627 AN: 3468

East Asian (EAS) AF: 0.405 AC: 2096 AN: 5180

South Asian (SAS) AF: 0.360 AC: 1733 AN: 4818

European-Finnish (FIN) AF: 0.424 AC: 4474 AN: 10556

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.440 AC: 29910 AN: 67936

Other (OTH) AF: 0.359 AC: 758 AN: 2114

Alfa AF: 0.415 Hom.: 22805

Bravo AF: 0.338

Asia WGS AF: 0.372 AC: 1294 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	9.3
DANN	Benign	0.33
PhyloP100		0.42
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10511668; hg19: chr9-19022470;