16-12091953-T-C

Variant names:

• chr16-12091953-T-C
• rs8048589
• NM_032167.5:c.1402+13038T>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.1402+13038T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 152,018 control chromosomes in the GnomAD database, including 4,327 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 0.24 (4327 hom., cov: 31)
• Consequence: SNX29 NM_032167.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.85
• Publications: 8 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.285 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.1402+13038T>C		intron	N/A	NP_115543.3
	SNX29	NM_001376490.1		c.1402+13038T>C		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.1402+13038T>C		intron	N/A	ENSP00000456480.1
	SNX29	ENST00000563308.1	TSL:5	c.301+13038T>C		intron	N/A	ENSP00000455747.1

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35852 AN: 151898 Hom.: 4319 Cov.: 31

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.236 AC: 35875 AN: 152018 Hom.: 4327 Cov.: 31 AF XY: 0.238 AC XY: 17684 AN XY: 74310

African (AFR) AF: 0.289 AC: 11981 AN: 41442

American (AMR) AF: 0.268 AC: 4098 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 548 AN: 3468

East Asian (EAS) AF: 0.216 AC: 1118 AN: 5166

South Asian (SAS) AF: 0.226 AC: 1085 AN: 4806

European-Finnish (FIN) AF: 0.194 AC: 2052 AN: 10572

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.208 AC: 14156 AN: 67980

Other (OTH) AF: 0.236 AC: 498 AN: 2110

Alfa AF: 0.228 Hom.: 2083

Bravo AF: 0.245

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.22
DANN	Benign	0.21
PhyloP100		-2.9
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: rs8048589; hg19: chr16-12185810;