rs117147010

Variant names:

• chr16-12503078-C-T
• rs117147010
• NM_032167.5:c.2179-21624C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

Genes affected

SNX29 (HGNC:30542): (sorting nexin 29) Predicted to enable phosphatidylinositol binding activity. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 59 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNX29	NM_032167.5	c.2179-21624C>T		intron_variant	Intron 19 of 20	ENST00000566228.6	NP_115543.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNX29	ENST00000566228.6	c.2179-21624C>T		intron_variant	Intron 19 of 20	5	NM_032167.5	ENSP00000456480.1
SNX29	ENST00000564791.5	c.646-21624C>T		intron_variant	Intron 7 of 8	1		ENSP00000457017.1

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

African (AFR) AF: 0.00960 AC: 399 AN: 41568

American (AMR) AF: 0.0252 AC: 386 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0593 AC: 206 AN: 3472

East Asian (EAS) AF: 0.000385 AC: 2 AN: 5190

South Asian (SAS) AF: 0.00766 AC: 37 AN: 4830

European-Finnish (FIN) AF: 0.0280 AC: 296 AN: 10588

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0311 AC: 2115 AN: 68014

Other (OTH) AF: 0.0350 AC: 74 AN: 2114

Alfa AF: 0.0279 Hom.: 82

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
PhyloP100		-2.5
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs117147010; hg19: chr16-12596935;