16-12547258-C-T

Variant names:

• chr16-12547258-C-T
• rs1641895
• NM_032167.5:c.2319-21248C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_032167.5(SNX29):​c.2319-21248C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0101 in 152,286 control chromosomes in the GnomAD database, including 9 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 0.010 (9 hom., cov: 33)
• Consequence: SNX29 NM_032167.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.660
• Publications: 7 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=-0.74).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0101 (1539/152286) while in subpopulation NFE AF = 0.0166 (1126/68018). AF 95% confidence interval is 0.0158. There are 9 homozygotes in GnomAd4. There are 689 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 9 AR gene

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNX29	NM_032167.5	MANE Select	c.2319-21248C>T		intron	N/A	NP_115543.3	Q8TEQ0-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNX29	ENST00000566228.6	TSL:5 MANE Select	c.2319-21248C>T		intron	N/A	ENSP00000456480.1	Q8TEQ0-1
	SNX29	ENST00000892126.1		c.2313-21248C>T		intron	N/A	ENSP00000562185.1
	SNX29	ENST00000892127.1		c.2286-21248C>T		intron	N/A	ENSP00000562186.1

Frequencies

GnomAD3 genomes AF: 0.0101 AC: 1540 AN: 152168 Hom.: 9 Cov.: 33

Gnomad AFR AF: 0.00246

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.00779

Gnomad ASJ AF: 0.00606

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00517

Gnomad FIN AF: 0.00687

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0166

Gnomad OTH AF: 0.00956

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

GnomAD4 genome AF: 0.0101 AC: 1539 AN: 152286 Hom.: 9 Cov.: 33 AF XY: 0.00925 AC XY: 689 AN XY: 74458

African (AFR) AF: 0.00245 AC: 102 AN: 41558

American (AMR) AF: 0.00778 AC: 119 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.00606 AC: 21 AN: 3468

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5180

South Asian (SAS) AF: 0.00518 AC: 25 AN: 4830

European-Finnish (FIN) AF: 0.00687 AC: 73 AN: 10624

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0166 AC: 1126 AN: 68018

Other (OTH) AF: 0.00946 AC: 20 AN: 2114

Alfa AF: 0.0148 Hom.: 48

Bravo AF: 0.0102

Asia WGS AF: 0.00346 AC: 12 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	5.7
DANN	Benign	0.76
PhyloP100		0.66
Mutation Taster		=100/0	polymorphism

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: rs1641895; hg19: chr16-12641115;