chr9-18969424-A-C

Variant names:

• chr9-18969424-A-C
• rs10511666
• NM_153707.4:c.39-18487T>G

Variant summary

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

The NM_153707.4(SAXO1):​c.39-18487T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 152,104 control chromosomes in the GnomAD database, including 6,990 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 0.20 (6990 hom., cov: 32)
• Consequence: SAXO1 NM_153707.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.286
• Publications: 1 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=-0.63).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SAXO1	NM_153707.4	c.39-18487T>G		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.39-18487T>G		intron_variant	Intron 1 of 3	1	NM_153707.4	ENSP00000369907.4

Frequencies

GnomAD3 genomes AF: 0.204 AC: 30987 AN: 151988 Hom.: 6966 Cov.: 32

Gnomad AFR AF: 0.564

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0896

Gnomad ASJ AF: 0.0524

Gnomad EAS AF: 0.0887

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.0864

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0541

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.204 AC: 31056 AN: 152104 Hom.: 6990 Cov.: 32 AF XY: 0.201 AC XY: 14930 AN XY: 74358

African (AFR) AF: 0.565 AC: 23396 AN: 41438

American (AMR) AF: 0.0895 AC: 1369 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0524 AC: 182 AN: 3470

East Asian (EAS) AF: 0.0885 AC: 458 AN: 5176

South Asian (SAS) AF: 0.135 AC: 648 AN: 4814

European-Finnish (FIN) AF: 0.0864 AC: 916 AN: 10598

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0542 AC: 3682 AN: 67994

Other (OTH) AF: 0.169 AC: 357 AN: 2108

Alfa AF: 0.102 Hom.: 2838

Bravo AF: 0.220

Asia WGS AF: 0.132 AC: 459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	14
DANN	Benign	0.53
PhyloP100		-0.29
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: rs10511666; hg19: chr9-18969422;