16-12399002-A-G

Variant names:

• chr16-12399002-A-G
• rs7203335
• NM_032167.5:c.1955+501A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032167.5(SNX29):​c.1955+501A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 152,106 control chromosomes in the GnomAD database, including 2,604 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 0.17 (2604 hom., cov: 32)
• Consequence: SNX29 NM_032167.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0930
• Publications: 5 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).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNX29	NM_032167.5	c.1955+501A>G		intron_variant	Intron 17 of 20	ENST00000566228.6	NP_115543.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNX29	ENST00000566228.6	c.1955+501A>G		intron_variant	Intron 17 of 20	5	NM_032167.5	ENSP00000456480.1
SNX29	ENST00000564791.5	c.422+501A>G		intron_variant	Intron 5 of 8	1		ENSP00000457017.1
SNX29	ENST00000562510.1	c.83+501A>G		intron_variant	Intron 2 of 3	3		ENSP00000455327.1

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26331 AN: 151986 Hom.: 2599 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.0985

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.173 AC: 26361 AN: 152106 Hom.: 2604 Cov.: 32 AF XY: 0.169 AC XY: 12531 AN XY: 74346

African (AFR) AF: 0.238 AC: 9871 AN: 41460

American (AMR) AF: 0.134 AC: 2048 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 921 AN: 3466

East Asian (EAS) AF: 0.00212 AC: 11 AN: 5178

South Asian (SAS) AF: 0.150 AC: 723 AN: 4818

European-Finnish (FIN) AF: 0.0985 AC: 1042 AN: 10578

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11096 AN: 68004

Other (OTH) AF: 0.179 AC: 376 AN: 2104

Alfa AF: 0.165 Hom.: 2921

Bravo AF: 0.179

Asia WGS AF: 0.0770 AC: 268 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	2.2
DANN	Benign	0.65
PhyloP100		0.093
Mutation Taster		=100/0	polymorphism (auto)

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: rs7203335; hg19: chr16-12492859;