rs1564286433

Variant names:

• chr9-112836361-C-A
• rs1564286433
• NM_001012994.2:c.766C>A

Your query was ambiguous. Multiple possible variants found:

• chr9-112836361-C-A
• chr9-112836361-C-G
• chr9-112836361-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001012994.2(SNX30):​c.766C>A​(p.Leu256Met) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L256V) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: SNX30 NM_001012994.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.17
• Publications: 0 publications found

Genes affected

SNX30 (HGNC:23685): (sorting nexin family member 30) Predicted to enable phosphatidylinositol binding activity. Predicted to be involved in protein transport. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001012994.2. 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
	SNX30	NM_001012994.2	MANE Select	c.766C>A	p.Leu256Met	missense	Exon 5 of 9	NP_001013012.1	Q5VWJ9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNX30	ENST00000374232.8	TSL:5 MANE Select	c.766C>A	p.Leu256Met	missense	Exon 5 of 9	ENSP00000363349.3	Q5VWJ9
	SNX30	ENST00000870319.1		c.574C>A	p.Leu192Met	missense	Exon 4 of 8	ENSP00000540378.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.16
BayesDel_addAF	Uncertain	0.037	T
BayesDel_noAF	Benign	-0.18
CADD	Uncertain	23
DANN	Uncertain	1.0
DEOGEN2	Benign	0.059	T
Eigen	Uncertain	0.63
Eigen_PC	Uncertain	0.62
FATHMM_MKL	Uncertain	0.94	D
LIST_S2	Benign	0.84	T
M_CAP	Benign	0.016	T
MetaRNN	Uncertain	0.65	D
MetaSVM	Benign	-0.82	T
MutationAssessor	Benign	0.97	L
PhyloP100		6.2
PrimateAI	Pathogenic	0.82	D
PROVEAN	Benign	-0.94	N
REVEL	Benign	0.17
Sift	Benign	0.24	T
Sift4G	Benign	0.35	T
Polyphen		1.0	D
Vest4		0.80
MutPred		0.41		Gain of catalytic residue at L256 (P = 0.0289)
MVP		0.32
MPC		1.0
ClinPred		0.94	D
GERP RS		4.8
Varity_R		0.33
gMVP		0.55
Mutation Taster		=59/41	polymorphism

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: rs1564286433; hg19: chr9-115598641;