16-12560005-A-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

LOC105371085 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNX29	NM_032167.5	c.2319-8501A>G		intron_variant		ENST00000566228.6
LOC105371085	XR_007064990.1	n.917T>C		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNX29	ENST00000566228.6	c.2319-8501A>G		intron_variant		5	NM_032167.5	P1

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

Gnomad4 AFR AF: 0.609

Gnomad4 AMR AF: 0.586

Gnomad4 ASJ AF: 0.813

Gnomad4 EAS AF: 0.193

Gnomad4 SAS AF: 0.515

Gnomad4 FIN AF: 0.672

Gnomad4 NFE AF: 0.771

Gnomad4 OTH AF: 0.711

Alfa AF: 0.740 Hom.: 91538

Bravo AF: 0.663

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.36
Dann	Benign	0.67

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: rs11863694; hg19: chr16-12653862;