rs3803602

chr16-12571104-G-Achr16-12571104-G-Cchr16-12571104-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.*2475G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0247 in 232,550 control chromosomes in the GnomAD database, including 471 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 0.022 (281 hom., cov: 33)
  • Exomes 𝑓: 0.029 (190 hom.)
• Consequence: SNX29 NM_032167.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.290

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNX29	NM_032167.5	c.*2475G>A		3_prime_UTR_variant	21/21	ENST00000566228.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNX29	ENST00000566228.6	c.*2475G>A		3_prime_UTR_variant	21/21	5	NM_032167.5	P1
	ENST00000564505.1	n.308-9958C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0223 AC: 3392 AN: 152154 Hom.: 280 Cov.: 33

Gnomad AFR AF: 0.00468

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.000576

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.0513

Gnomad FIN AF: 0.0103

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00151

Gnomad OTH AF: 0.0244

GnomAD4 exome AF: 0.0294 AC: 2359 AN: 80278 Hom.: 190 Cov.: 0 AF XY: 0.0269 AC XY: 994 AN XY: 36906

Gnomad4 AFR exome AF: 0.00388

Gnomad4 AMR exome AF: 0.141

Gnomad4 ASJ exome AF: 0.00118

Gnomad4 EAS exome AF: 0.155

Gnomad4 SAS exome AF: 0.0460

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00107

Gnomad4 OTH exome AF: 0.0230

GnomAD4 genome AF: 0.0223 AC: 3393 AN: 152272 Hom.: 281 Cov.: 33 AF XY: 0.0256 AC XY: 1906 AN XY: 74458

Gnomad4 AFR AF: 0.00467

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.000576

Gnomad4 EAS AF: 0.197

Gnomad4 SAS AF: 0.0514

Gnomad4 FIN AF: 0.0103

Gnomad4 NFE AF: 0.00151

Gnomad4 OTH AF: 0.0247

Alfa AF: 0.00966 Hom.: 224

Bravo AF: 0.0336

Asia WGS AF: 0.119 AC: 411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	2.0
Dann	Benign	0.57

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: rs3803602; hg19: chr16-12664961;