rs10511668

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr9-19022472-C-G
• chr9-19022472-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_153707.4(SAXO1):​c.38+10399G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

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.38+10399G>C		intron	N/A	NP_714918.2	Q8IYX7
	SAXO1	NM_001287049.2		c.-158+26737G>C		intron	N/A	NP_001273978.1	F6S232
	SAXO1	NM_001287050.2		c.38+10399G>C		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.38+10399G>C		intron	N/A	ENSP00000369907.4	Q8IYX7
	SAXO1	ENST00000542071.2	TSL:3	c.-158+26737G>C		intron	N/A	ENSP00000438823.2	F6S232
	SAXO1	ENST00000649457.1		c.-158+26737G>C		intron	N/A	ENSP00000497677.1	F6S232

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.9
DANN	Benign	0.40
PhyloP100		0.42

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10511668;

hg19: chr9-19022470;