16-12251327-T-G

Variant names:

• chr16-12251327-T-G
• rs7195058
• NM_032167.5:c.1679-26606T>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032167.5(SNX29):​c.1679-26606T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.652 in 152,124 control chromosomes in the GnomAD database, including 33,438 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 0.65 (33438 hom., cov: 33)
• Consequence: SNX29 NM_032167.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNX29	NM_032167.5	c.1679-26606T>G		intron_variant	Intron 14 of 20	ENST00000566228.6	NP_115543.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNX29	ENST00000566228.6	c.1679-26606T>G		intron_variant	Intron 14 of 20	5	NM_032167.5	ENSP00000456480.1
SNX29	ENST00000564791.5	c.146-26606T>G		intron_variant	Intron 2 of 8	1		ENSP00000457017.1

Frequencies

GnomAD3 genomes AF: 0.652 AC: 99158 AN: 152006 Hom.: 33384 Cov.: 33

Gnomad AFR AF: 0.821

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.610

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.598

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

GnomAD4 genome AF: 0.652 AC: 99254 AN: 152124 Hom.: 33438 Cov.: 33 AF XY: 0.640 AC XY: 47578 AN XY: 74354

Gnomad4 AFR AF: 0.821

Gnomad4 AMR AF: 0.609

Gnomad4 ASJ AF: 0.641

Gnomad4 EAS AF: 0.631

Gnomad4 SAS AF: 0.335

Gnomad4 FIN AF: 0.495

Gnomad4 NFE AF: 0.611

Gnomad4 OTH AF: 0.591

Alfa AF: 0.614 Hom.: 40318

Bravo AF: 0.672

Asia WGS AF: 0.461 AC: 1603 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.2
DANN	Benign	0.30

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: rs7195058; hg19: chr16-12345184;