rs442332

Positions:

• chr16-11978267-G-A
• chr16-11978267-G-C
• chr16-11978267-G-T

Variant summary

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

The NM_032167.5(SNX29):​c.7+1454G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.871 in 152,212 control chromosomes in the GnomAD database, including 58,246 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 (58246 hom., cov: 32)
• Consequence: SNX29 NM_032167.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53

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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNX29	NM_032167.5	c.7+1454G>A		intron_variant		ENST00000566228.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNX29	ENST00000566228.6	c.7+1454G>A		intron_variant		5	NM_032167.5	P1
SNX29	ENST00000569801.5	c.7+1454G>A		intron_variant, NMD_transcript_variant		4
SNX29	ENST00000564111.5	n.69+1454G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.871 AC: 132429 AN: 152094 Hom.: 58210 Cov.: 32

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.952

Gnomad AMR AF: 0.833

Gnomad ASJ AF: 0.909

Gnomad EAS AF: 0.933

Gnomad SAS AF: 0.945

Gnomad FIN AF: 0.951

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.928

Gnomad OTH AF: 0.888

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

GnomAD4 genome AF: 0.871 AC: 132519 AN: 152212 Hom.: 58246 Cov.: 32 AF XY: 0.874 AC XY: 65043 AN XY: 74428

Gnomad4 AFR AF: 0.747

Gnomad4 AMR AF: 0.832

Gnomad4 ASJ AF: 0.909

Gnomad4 EAS AF: 0.933

Gnomad4 SAS AF: 0.945

Gnomad4 FIN AF: 0.951

Gnomad4 NFE AF: 0.928

Gnomad4 OTH AF: 0.884

Alfa AF: 0.897 Hom.: 10681

Bravo AF: 0.851

Asia WGS AF: 0.898 AC: 3123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.21
DANN	Benign	0.36

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: rs442332; hg19: chr16-12072124;