16-11983775-A-G

Position:

• chr16-11983775-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.7+6962A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 882,744 control chromosomes in the GnomAD database, including 46,866 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 0.34 (9286 hom., cov: 31)
  • Exomes 𝑓: 0.32 (37580 hom.)
• Consequence: SNX29 NM_032167.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.489

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.624 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SNX29	NM_032167.5	c.7+6962A>G		intron_variant		ENST00000566228.6	NP_115543.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SNX29	ENST00000566228.6	c.7+6962A>G		intron_variant		5	NM_032167.5	ENSP00000456480	P1
SNX29	ENST00000569801.5	c.7+6962A>G		intron_variant, NMD_transcript_variant		4		ENSP00000457085
SNX29	ENST00000564111.5	n.69+6962A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51652 AN: 151938 Hom.: 9279 Cov.: 31

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.643

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.317

GnomAD4 exome AF: 0.317 AC: 231346 AN: 730688 Hom.: 37580 AF XY: 0.316 AC XY: 107372 AN XY: 339774

Gnomad4 AFR exome AF: 0.309

Gnomad4 AMR exome AF: 0.342

Gnomad4 ASJ exome AF: 0.214

Gnomad4 EAS exome AF: 0.644

Gnomad4 SAS exome AF: 0.528

Gnomad4 FIN exome AF: 0.399

Gnomad4 NFE exome AF: 0.311

Gnomad4 OTH exome AF: 0.333

GnomAD4 genome AF: 0.340 AC: 51686 AN: 152056 Hom.: 9286 Cov.: 31 AF XY: 0.349 AC XY: 25942 AN XY: 74300

Gnomad4 AFR AF: 0.309

Gnomad4 AMR AF: 0.336

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.643

Gnomad4 SAS AF: 0.546

Gnomad4 FIN AF: 0.390

Gnomad4 NFE AF: 0.322

Gnomad4 OTH AF: 0.320

Alfa AF: 0.332 Hom.: 4103

Bravo AF: 0.327

Asia WGS AF: 0.531 AC: 1843 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.6
DANN	Benign	0.85

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: rs12922317; hg19: chr16-12077632;