16-12560005-A-G

Variant names:

• chr16-12560005-A-G
• rs11863694
• NM_032167.5:c.2319-8501A>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.2319-8501A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.674 in 152,036 control chromosomes in the GnomAD database, including 35,908 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 0.67 (35908 hom., cov: 31)
• Consequence: SNX29 NM_032167.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.467
• Publications: 6 publications found

Genes affected

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

SNX29-AS3 (HGNC:58619):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.766 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032167.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNX29	NM_032167.5	MANE Select	c.2319-8501A>G		intron	N/A	NP_115543.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNX29	ENST00000566228.6	TSL:5 MANE Select	c.2319-8501A>G		intron	N/A	ENSP00000456480.1

Frequencies

GnomAD3 genomes AF: 0.674 AC: 102420 AN: 151918 Hom.: 35897 Cov.: 31

Gnomad AFR AF: 0.609

Gnomad AMI AF: 0.770

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.813

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.771

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.674 AC: 102475 AN: 152036 Hom.: 35908 Cov.: 31 AF XY: 0.664 AC XY: 49320 AN XY: 74326

African (AFR) AF: 0.609 AC: 25251 AN: 41456

American (AMR) AF: 0.586 AC: 8956 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.813 AC: 2821 AN: 3472

East Asian (EAS) AF: 0.193 AC: 997 AN: 5176

South Asian (SAS) AF: 0.515 AC: 2481 AN: 4814

European-Finnish (FIN) AF: 0.672 AC: 7090 AN: 10544

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.771 AC: 52433 AN: 67978

Other (OTH) AF: 0.711 AC: 1499 AN: 2108

Alfa AF: 0.729 Hom.: 128670

Bravo AF: 0.663

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.36
DANN	Benign	0.67
PhyloP100		-0.47
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: rs11863694; hg19: chr16-12653862;