16-12264349-C-T

Position:

• chr16-12264349-C-T

Variant summary

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

The NM_032167.5(SNX29):​c.1679-13584C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.635 in 152,184 control chromosomes in the GnomAD database, including 31,718 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 0.64 (31718 hom., cov: 33)
• Consequence: SNX29 NM_032167.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.697

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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SNX29	NM_032167.5	c.1679-13584C>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.1679-13584C>T		intron_variant		5	NM_032167.5	ENSP00000456480.1
SNX29	ENST00000564791.5	c.146-13584C>T		intron_variant		1		ENSP00000457017.1

Frequencies

GnomAD3 genomes AF: 0.635 AC: 96598 AN: 152066 Hom.: 31668 Cov.: 33

Gnomad AFR AF: 0.775

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.658

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.635 AC: 96694 AN: 152184 Hom.: 31718 Cov.: 33 AF XY: 0.620 AC XY: 46129 AN XY: 74388

Gnomad4 AFR AF: 0.776

Gnomad4 AMR AF: 0.620

Gnomad4 ASJ AF: 0.658

Gnomad4 EAS AF: 0.445

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.458

Gnomad4 NFE AF: 0.620

Gnomad4 OTH AF: 0.584

Alfa AF: 0.621 Hom.: 60995

Bravo AF: 0.657

Asia WGS AF: 0.395 AC: 1374 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.21
DANN	Benign	0.72

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: rs905950; hg19: chr16-12358206;