rs7857590

Variant names:

• chr9-18989895-T-A
• rs7857590
• NM_153707.4:c.39-38958A>T

Variant summary

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

The NM_153707.4(SAXO1):​c.39-38958A>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
• Publications: 3 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_153707.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SAXO1	NM_153707.4	MANE Select	c.39-38958A>T		intron	N/A	NP_714918.2	Q8IYX7
	SAXO1	NM_001287049.2		c.-157-38958A>T		intron	N/A	NP_001273978.1	F6S232
	SAXO1	NM_001287050.2		c.39-38958A>T		intron	N/A	NP_001273979.1	Q5VZT6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SAXO1	ENST00000380534.9	TSL:1 MANE Select	c.39-38958A>T		intron	N/A	ENSP00000369907.4	Q8IYX7
	SAXO1	ENST00000542071.2	TSL:3	c.-157-38958A>T		intron	N/A	ENSP00000438823.2	F6S232
	SAXO1	ENST00000649457.1		c.-157-38958A>T		intron	N/A	ENSP00000497677.1	F6S232

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

African (AFR) AF: 0.435 AC: 18058 AN: 41470

American (AMR) AF: 0.536 AC: 8200 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.669 AC: 2320 AN: 3470

East Asian (EAS) AF: 0.521 AC: 2690 AN: 5168

South Asian (SAS) AF: 0.511 AC: 2464 AN: 4824

European-Finnish (FIN) AF: 0.616 AC: 6511 AN: 10562

Middle Eastern (MID) AF: 0.514 AC: 150 AN: 292

European-Non Finnish (NFE) AF: 0.633 AC: 43015 AN: 67980

Other (OTH) AF: 0.550 AC: 1159 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.33
DANN	Benign	0.37
PhyloP100		-0.44
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7857590; hg19: chr9-18989893; COSMIC: COSV65869213;