rs8048589

Positions:

• chr16-12091953-T-C

Variant summary

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

The NM_032167.5(SNX29):​c.1402+13038T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 152,018 control chromosomes in the GnomAD database, including 4,327 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 0.24 (4327 hom., cov: 31)
• Consequence: SNX29 NM_032167.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.85

Genes affected

SNX29 (HGNC:30542): (sorting nexin 29) Predicted to enable phosphatidylinositol binding activity. [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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNX29	NM_032167.5	c.1402+13038T>C		intron_variant		ENST00000566228.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNX29	ENST00000566228.6	c.1402+13038T>C		intron_variant		5	NM_032167.5	P1
SNX29	ENST00000563308.1	c.303+13038T>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35852 AN: 151898 Hom.: 4319 Cov.: 31

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.236 AC: 35875 AN: 152018 Hom.: 4327 Cov.: 31 AF XY: 0.238 AC XY: 17684 AN XY: 74310

Gnomad4 AFR AF: 0.289

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.158

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.194

Gnomad4 NFE AF: 0.208

Gnomad4 OTH AF: 0.236

Alfa AF: 0.220 Hom.: 651

Bravo AF: 0.245

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.22
DANN	Benign	0.21

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: rs8048589; hg19: chr16-12185810;