rs7191435

chr16-12269178-C-T

Variant summary

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

The NM_032167.5(SNX29):c.1679-8755C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.697 in 152,170 control chromosomes in the GnomAD database, including 38,041 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 0.70 (38041 hom., cov: 33)
• Consequence: SNX29 NM_032167.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.854 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNX29	NM_032167.5	c.1679-8755C>T		intron_variant		ENST00000566228.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNX29	ENST00000566228.6	c.1679-8755C>T		intron_variant		5	NM_032167.5	P1
SNX29	ENST00000564791.5	c.146-8755C>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.697 AC: 105967 AN: 152052 Hom.: 37983 Cov.: 33

Gnomad AFR AF: 0.861

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.736

Gnomad EAS AF: 0.786

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.650

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

GnomAD4 genome AF: 0.697 AC: 106075 AN: 152170 Hom.: 38041 Cov.: 33 AF XY: 0.685 AC XY: 50979 AN XY: 74408

Gnomad4 AFR AF: 0.861

Gnomad4 AMR AF: 0.648

Gnomad4 ASJ AF: 0.736

Gnomad4 EAS AF: 0.786

Gnomad4 SAS AF: 0.422

Gnomad4 FIN AF: 0.519

Gnomad4 NFE AF: 0.649

Gnomad4 OTH AF: 0.645

Alfa AF: 0.663 Hom.: 67262

Bravo AF: 0.718

Asia WGS AF: 0.616 AC: 2141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.10
Dann	Benign	0.49

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: rs7191435; hg19: chr16-12363035;