rs10500380

Variant names:

• chr16-12293419-T-C
• rs10500380
• NM_032167.5:c.1782+15383T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032167.5(SNX29):​c.1782+15383T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0321 in 152,312 control chromosomes in the GnomAD database, including 126 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 0.032 (126 hom., cov: 32)
• Consequence: SNX29 NM_032167.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0598 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNX29	NM_032167.5	c.1782+15383T>C		intron_variant	Intron 15 of 20	ENST00000566228.6	NP_115543.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNX29	ENST00000566228.6	c.1782+15383T>C		intron_variant	Intron 15 of 20	5	NM_032167.5	ENSP00000456480.1
SNX29	ENST00000564791.5	c.249+15383T>C		intron_variant	Intron 3 of 8	1		ENSP00000457017.1

Frequencies

GnomAD3 genomes AF: 0.0320 AC: 4873 AN: 152194 Hom.: 126 Cov.: 32

Gnomad AFR AF: 0.0604

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0628

Gnomad ASJ AF: 0.0383

Gnomad EAS AF: 0.0221

Gnomad SAS AF: 0.0104

Gnomad FIN AF: 0.000942

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0152

Gnomad OTH AF: 0.0268

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

GnomAD4 genome AF: 0.0321 AC: 4886 AN: 152312 Hom.: 126 Cov.: 32 AF XY: 0.0324 AC XY: 2410 AN XY: 74474

African (AFR) AF: 0.0603 AC: 2508 AN: 41564

American (AMR) AF: 0.0631 AC: 966 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0383 AC: 133 AN: 3470

East Asian (EAS) AF: 0.0221 AC: 115 AN: 5194

South Asian (SAS) AF: 0.0108 AC: 52 AN: 4826

European-Finnish (FIN) AF: 0.000942 AC: 10 AN: 10612

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0152 AC: 1035 AN: 68026

Other (OTH) AF: 0.0265 AC: 56 AN: 2112

Alfa AF: 0.0239 Hom.: 73

Bravo AF: 0.0378

Asia WGS AF: 0.0210 AC: 72 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.16
DANN	Benign	0.32
PhyloP100		-1.7
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: rs10500380; hg19: chr16-12387276;