rs4781213

Positions:

• chr16-12367560-C-A
• chr16-12367560-C-G

Variant summary

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

The NM_032167.5(SNX29):​c.1899+11281C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.87 in 152,270 control chromosomes in the GnomAD database, including 57,778 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 0.87 (57778 hom., cov: 34)
  • Failed GnomAD Quality Control
• Consequence: SNX29 NM_032167.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0420

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.899 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SNX29	NM_032167.5	c.1899+11281C>A		intron_variant		ENST00000566228.6	NP_115543.3
LOC101927227	XR_243354.4	n.71-91G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SNX29	ENST00000566228.6	c.1899+11281C>A		intron_variant		5	NM_032167.5	ENSP00000456480	P1
SNX29	ENST00000564791.5	c.366+11281C>A		intron_variant		1		ENSP00000457017
	ENST00000569490.1	n.52-91G>T		intron_variant, non_coding_transcript_variant		3
SNX29	ENST00000562510.1	c.27+11281C>A		intron_variant		3		ENSP00000455327

Frequencies

GnomAD3 genomes AF: 0.870 AC: 132297 AN: 152152 Hom.: 57722 Cov.: 34

Gnomad AFR AF: 0.904

Gnomad AMI AF: 0.764

Gnomad AMR AF: 0.882

Gnomad ASJ AF: 0.896

Gnomad EAS AF: 0.921

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.789

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.869

Gnomad OTH AF: 0.881

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

GnomAD4 genome AF: 0.870 AC: 132411 AN: 152270 Hom.: 57778 Cov.: 34 AF XY: 0.864 AC XY: 64300 AN XY: 74438

Gnomad4 AFR AF: 0.904

Gnomad4 AMR AF: 0.883

Gnomad4 ASJ AF: 0.896

Gnomad4 EAS AF: 0.921

Gnomad4 SAS AF: 0.655

Gnomad4 FIN AF: 0.789

Gnomad4 NFE AF: 0.869

Gnomad4 OTH AF: 0.883

Alfa AF: 0.872 Hom.: 74119

Bravo AF: 0.882

Asia WGS AF: 0.801 AC: 2780 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	2.4
DANN	Benign	0.63

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: rs4781213; hg19: chr16-12461417;