16-12560551-G-C

Variant names:

• chr16-12560551-G-C
• rs11639949
• NM_032167.5:c.2319-7955G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032167.5(SNX29):​c.2319-7955G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 152,030 control chromosomes in the GnomAD database, including 3,431 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 0.21 (3431 hom., cov: 32)
• Consequence: SNX29 NM_032167.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0740
• Publications: 3 publications found

Genes affected

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

SNX29-AS3 (HGNC:58619):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.415 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.2319-7955G>C		intron	N/A	NP_115543.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNX29	ENST00000566228.6	TSL:5 MANE Select	c.2319-7955G>C		intron	N/A	ENSP00000456480.1
	ENSG00000259899	ENST00000564505.2	TSL:3	n.*200C>G		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31544 AN: 151912 Hom.: 3432 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.186

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.208 AC: 31567 AN: 152030 Hom.: 3431 Cov.: 32 AF XY: 0.210 AC XY: 15632 AN XY: 74326

African (AFR) AF: 0.203 AC: 8427 AN: 41434

American (AMR) AF: 0.187 AC: 2856 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 622 AN: 3468

East Asian (EAS) AF: 0.430 AC: 2214 AN: 5148

South Asian (SAS) AF: 0.231 AC: 1109 AN: 4802

European-Finnish (FIN) AF: 0.237 AC: 2508 AN: 10584

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.194 AC: 13203 AN: 67990

Other (OTH) AF: 0.185 AC: 391 AN: 2110

Alfa AF: 0.0832 Hom.: 145

Bravo AF: 0.203

Asia WGS AF: 0.314 AC: 1091 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.43
PhyloP100		0.074
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: rs11639949; hg19: chr16-12654408;