16-12097090-G-C

Position:

• chr16-12097090-G-C

Variant summary

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

The NM_032167.5(SNX29):​c.1402+18175G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.677 in 152,132 control chromosomes in the GnomAD database, including 36,542 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 0.68 (36542 hom., cov: 32)
• Consequence: SNX29 NM_032167.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74

Genes affected

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

SNX29 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.896 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SNX29	NM_032167.5	c.1402+18175G>C		intron_variant		ENST00000566228.6	NP_115543.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SNX29	ENST00000566228.6	c.1402+18175G>C		intron_variant		5	NM_032167.5	ENSP00000456480.1
SNX29	ENST00000563308.1	c.301+18175G>C		intron_variant		5		ENSP00000455747.1

Frequencies

GnomAD3 genomes AF: 0.677 AC: 102934 AN: 152014 Hom.: 36485 Cov.: 32

Gnomad AFR AF: 0.881

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.689

Gnomad EAS AF: 0.918

Gnomad SAS AF: 0.629

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.677 AC: 103051 AN: 152132 Hom.: 36542 Cov.: 32 AF XY: 0.675 AC XY: 50192 AN XY: 74362

Gnomad4 AFR AF: 0.881

Gnomad4 AMR AF: 0.649

Gnomad4 ASJ AF: 0.689

Gnomad4 EAS AF: 0.918

Gnomad4 SAS AF: 0.629

Gnomad4 FIN AF: 0.492

Gnomad4 NFE AF: 0.573

Gnomad4 OTH AF: 0.690

Alfa AF: 0.461 Hom.: 1102

Bravo AF: 0.703

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.34
DANN	Benign	0.43

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: rs350232; hg19: chr16-12190947;