rs1539339

chr9-112831449-A-Cchr9-112831449-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001012994.2(SNX30):c.618+566A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 152,180 control chromosomes in the GnomAD database, including 4,738 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 0.22 (4738 hom., cov: 32)
• Consequence: SNX30 NM_001012994.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0130

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNX30	NM_001012994.2	c.618+566A>C		intron_variant		ENST00000374232.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNX30	ENST00000374232.8	c.618+566A>C		intron_variant		5	NM_001012994.2	P1

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33807 AN: 152062 Hom.: 4738 Cov.: 32

Gnomad AFR AF: 0.0522

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.222 AC: 33811 AN: 152180 Hom.: 4738 Cov.: 32 AF XY: 0.223 AC XY: 16593 AN XY: 74378

Gnomad4 AFR AF: 0.0520

Gnomad4 AMR AF: 0.278

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.406

Gnomad4 SAS AF: 0.260

Gnomad4 FIN AF: 0.248

Gnomad4 NFE AF: 0.291

Gnomad4 OTH AF: 0.224

Alfa AF: 0.266 Hom.: 9814

Bravo AF: 0.216

Asia WGS AF: 0.294 AC: 1024 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	1.3
Dann	Benign	0.78

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

Publications

LitVar

Other links and lift over

dbSNP: rs1539339; hg19: chr9-115593729;