9-18930882-T-G

Variant names:

• chr9-18930882-T-G
• rs4977469
• NM_153707.4:c.422-1827A>C

Variant summary

Our verdict is Benign. The variant received -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
• 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=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.843 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SAXO1	NM_153707.4	MANE Select	c.422-1827A>C		intron	N/A	NP_714918.2
	SAXO1	NM_001287049.2		c.227-1827A>C		intron	N/A	NP_001273978.1
	SAXO1	NM_001287050.2		c.219-1827A>C		intron	N/A	NP_001273979.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SAXO1	ENST00000380534.9	TSL:1 MANE Select	c.422-1827A>C		intron	N/A	ENSP00000369907.4
	SAXO1	ENST00000542071.2	TSL:3	c.227-1827A>C		intron	N/A	ENSP00000438823.2
	SAXO1	ENST00000649457.1		c.227-1827A>C		intron	N/A	ENSP00000497677.1

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

African (AFR) AF: 0.734 AC: 30445 AN: 41476

American (AMR) AF: 0.842 AC: 12881 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.830 AC: 2883 AN: 3472

East Asian (EAS) AF: 0.702 AC: 3618 AN: 5152

South Asian (SAS) AF: 0.839 AC: 4047 AN: 4824

European-Finnish (FIN) AF: 0.821 AC: 8685 AN: 10578

Middle Eastern (MID) AF: 0.871 AC: 256 AN: 294

European-Non Finnish (NFE) AF: 0.849 AC: 57711 AN: 67992

Other (OTH) AF: 0.819 AC: 1729 AN: 2110

Alfa AF: 0.834 Hom.: 162594

Bravo AF: 0.805

Asia WGS AF: 0.774 AC: 2688 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.97
DANN	Benign	0.38
PhyloP100		-0.22
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: rs4977469; hg19: chr9-18930880; COSMIC: COSV65871756;