NM_032167.5:c.7+6962A>G

Variant names:

• chr16-11983775-A-G
• rs12922317
• NM_032167.5:c.7+6962A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 19 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032167.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNX29	NM_032167.5	MANE Select	c.7+6962A>G		intron	N/A	NP_115543.3
	SNX29	NM_001376490.1		c.7+6962A>G		intron	N/A	NP_001363419.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNX29	ENST00000566228.6	TSL:5 MANE Select	c.7+6962A>G		intron	N/A	ENSP00000456480.1
	SNX29	ENST00000892126.1		c.7+6962A>G		intron	N/A	ENSP00000562185.1
	SNX29	ENST00000892127.1		c.7+6962A>G		intron	N/A	ENSP00000562186.1

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

African (AFR) AF: 0.309 AC: 4215 AN: 13638

American (AMR) AF: 0.342 AC: 286 AN: 836

Ashkenazi Jewish (ASJ) AF: 0.214 AC: 975 AN: 4546

East Asian (EAS) AF: 0.644 AC: 2028 AN: 3150

South Asian (SAS) AF: 0.528 AC: 7635 AN: 14466

European-Finnish (FIN) AF: 0.399 AC: 95 AN: 238

Middle Eastern (MID) AF: 0.326 AC: 470 AN: 1442

European-Non Finnish (NFE) AF: 0.311 AC: 207678 AN: 668488

Other (OTH) AF: 0.333 AC: 7964 AN: 23884

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

African (AFR) AF: 0.309 AC: 12824 AN: 41466

American (AMR) AF: 0.336 AC: 5126 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 769 AN: 3472

East Asian (EAS) AF: 0.643 AC: 3322 AN: 5170

South Asian (SAS) AF: 0.546 AC: 2633 AN: 4824

European-Finnish (FIN) AF: 0.390 AC: 4116 AN: 10552

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.322 AC: 21872 AN: 67992

Other (OTH) AF: 0.320 AC: 675 AN: 2112

Alfa AF: 0.326 Hom.: 6331

Bravo AF: 0.327

Asia WGS AF: 0.531 AC: 1843 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.6
DANN	Benign	0.85
PhyloP100		0.49
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12922317; hg19: chr16-12077632;