rs117147010

Positions:

• chr16-12503078-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_032167.5(SNX29):​c.2179-21624C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0234 in 152,286 control chromosomes in the GnomAD database, including 59 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 0.023 (59 hom., cov: 32)
• Consequence: SNX29 NM_032167.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.50

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=-0.95).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0234 (3571/152286) while in subpopulation NFE AF= 0.0311 (2115/68014). AF 95% confidence interval is 0.03. There are 59 homozygotes in gnomad4. There are 1669 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 59 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SNX29	NM_032167.5	c.2179-21624C>T		intron_variant		ENST00000566228.6	NP_115543.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SNX29	ENST00000566228.6	c.2179-21624C>T		intron_variant		5	NM_032167.5	ENSP00000456480	P1
SNX29	ENST00000564791.5	c.646-21624C>T		intron_variant		1		ENSP00000457017

Frequencies

GnomAD3 genomes AF: 0.0235 AC: 3576 AN: 152168 Hom.: 59 Cov.: 32

Gnomad AFR AF: 0.00968

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.0253

Gnomad ASJ AF: 0.0593

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.00745

Gnomad FIN AF: 0.0280

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0311

Gnomad OTH AF: 0.0354

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

GnomAD4 genome AF: 0.0234 AC: 3571 AN: 152286 Hom.: 59 Cov.: 32 AF XY: 0.0224 AC XY: 1669 AN XY: 74456

Gnomad4 AFR AF: 0.00960

Gnomad4 AMR AF: 0.0252

Gnomad4 ASJ AF: 0.0593

Gnomad4 EAS AF: 0.000385

Gnomad4 SAS AF: 0.00766

Gnomad4 FIN AF: 0.0280

Gnomad4 NFE AF: 0.0311

Gnomad4 OTH AF: 0.0350

Alfa AF: 0.0274 Hom.: 9

Bravo AF: 0.0227

Asia WGS AF: 0.00779 AC: 27 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.0080
DANN	Benign	0.38

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: rs117147010; hg19: chr16-12596935;