16-12560551-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.2319-7955G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 152,030 control chromosomes in the GnomAD database, including 3,431 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 0.21 (3431 hom., cov: 32)
• Consequence: SNX29 NM_032167.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0740

Genes affected

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

LOC105371085 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.415 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNX29	NM_032167.5	c.2319-7955G>C		intron_variant		ENST00000566228.6
LOC105371085	XR_007064990.1	n.371C>G		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNX29	ENST00000566228.6	c.2319-7955G>C		intron_variant		5	NM_032167.5	P1

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31544 AN: 151912 Hom.: 3432 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.208 AC: 31567 AN: 152030 Hom.: 3431 Cov.: 32 AF XY: 0.210 AC XY: 15632 AN XY: 74326

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.187

Gnomad4 ASJ AF: 0.179

Gnomad4 EAS AF: 0.430

Gnomad4 SAS AF: 0.231

Gnomad4 FIN AF: 0.237

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.185

Alfa AF: 0.0832 Hom.: 145

Bravo AF: 0.203

Asia WGS AF: 0.314 AC: 1091 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.1
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: rs11639949; hg19: chr16-12654408;