rs7857590

Positions:

• chr9-18989895-T-A

Variant summary

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

The NM_153707.4(SAXO1):​c.39-38958A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.559 in 152,074 control chromosomes in the GnomAD database, including 24,283 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 0.56 (24283 hom., cov: 32)
• Consequence: SAXO1 NM_153707.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.437

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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SAXO1	NM_153707.4	c.39-38958A>T		intron_variant		ENST00000380534.9	NP_714918.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SAXO1	ENST00000380534.9	c.39-38958A>T		intron_variant		1	NM_153707.4	ENSP00000369907.4

Frequencies

GnomAD3 genomes AF: 0.560 AC: 85041 AN: 151956 Hom.: 24285 Cov.: 32

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.669

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.616

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.555

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

GnomAD4 genome AF: 0.559 AC: 85071 AN: 152074 Hom.: 24283 Cov.: 32 AF XY: 0.558 AC XY: 41494 AN XY: 74348

Gnomad4 AFR AF: 0.435

Gnomad4 AMR AF: 0.536

Gnomad4 ASJ AF: 0.669

Gnomad4 EAS AF: 0.521

Gnomad4 SAS AF: 0.511

Gnomad4 FIN AF: 0.616

Gnomad4 NFE AF: 0.633

Gnomad4 OTH AF: 0.550

Alfa AF: 0.601 Hom.: 3489

Bravo AF: 0.548

Asia WGS AF: 0.507 AC: 1762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.33
DANN	Benign	0.37

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs7857590; hg19: chr9-18989893; COSMIC: COSV65869213;