16-12048583-C-T

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_Strong BP6_Moderate BP7 BS2

The NM_032167.5(SNX29):c.711C>T(p.Thr237=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00229 in 1,613,844 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0015 (1 hom., cov: 31)
  • Exomes 𝑓: 0.0024 (10 hom.)
• Consequence: SNX29 NM_032167.5 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.41

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 -11 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BP6: Variant 16-12048583-C-T is Benign according to our data. Variant chr16-12048583-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2646234.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-1.41 with no splicing effect.
• BS2: High Homozygotes in GnomAdExome at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNX29	NM_032167.5	c.711C>T	p.Thr237=	synonymous_variant	7/21	ENST00000566228.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNX29	ENST00000566228.6	c.711C>T	p.Thr237=	synonymous_variant	7/21	5	NM_032167.5	P1
SNX29	ENST00000564111.5	n.773C>T		non_coding_transcript_exon_variant	7/8	2
SNX29	ENST00000568359.1	n.542C>T		non_coding_transcript_exon_variant	4/5	5

Frequencies

GnomAD3 genomes AF: 0.00151 AC: 230 AN: 152062 Hom.: 1 Cov.: 31

Gnomad AFR AF: 0.000338

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.00210

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000415

Gnomad FIN AF: 0.000567

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00215

Gnomad OTH AF: 0.000478

GnomAD3 exomes AF: 0.00179 AC: 450 AN: 251100 Hom.: 2 AF XY: 0.00178 AC XY: 241 AN XY: 135716

Gnomad AFR exome AF: 0.000492

Gnomad AMR exome AF: 0.000752

Gnomad ASJ exome AF: 0.000198

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000392

Gnomad FIN exome AF: 0.00115

Gnomad NFE exome AF: 0.00325

Gnomad OTH exome AF: 0.00147

GnomAD4 exome AF: 0.00237 AC: 3464 AN: 1461664 Hom.: 10 Cov.: 33 AF XY: 0.00227 AC XY: 1648 AN XY: 727144

Gnomad4 AFR exome AF: 0.000388

Gnomad4 AMR exome AF: 0.000581

Gnomad4 ASJ exome AF: 0.000230

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000603

Gnomad4 FIN exome AF: 0.000936

Gnomad4 NFE exome AF: 0.00291

Gnomad4 OTH exome AF: 0.00141

GnomAD4 genome AF: 0.00151 AC: 230 AN: 152180 Hom.: 1 Cov.: 31 AF XY: 0.00144 AC XY: 107 AN XY: 74388

Gnomad4 AFR AF: 0.000337

Gnomad4 AMR AF: 0.00209

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000415

Gnomad4 FIN AF: 0.000567

Gnomad4 NFE AF: 0.00215

Gnomad4 OTH AF: 0.000473

Alfa AF: 0.00162 Hom.: 0

Bravo AF: 0.00187

EpiCase AF: 0.00196

EpiControl AF: 0.00219

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Mar 01, 2022

SNX29: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	1.5
Dann	Benign	0.65
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs147618832; hg19: chr16-12142440;