rs1641895

chr16-12547258-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_032167.5(SNX29):c.2319-21248C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0101 in 152,286 control chromosomes in the GnomAD database, including 9 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 0.010 (9 hom., cov: 33)
• Consequence: SNX29 NM_032167.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.660

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=-0.74).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0101 (1539/152286) while in subpopulation NFE AF= 0.0166 (1126/68018). AF 95% confidence interval is 0.0158. There are 9 homozygotes in gnomad4. There are 689 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 9 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNX29	NM_032167.5	c.2319-21248C>T		intron_variant		ENST00000566228.6
LOC105371085	XR_007064990.1	n.11778G>A		non_coding_transcript_exon_variant	2/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNX29	ENST00000566228.6	c.2319-21248C>T		intron_variant		5	NM_032167.5	P1

Frequencies

GnomAD3 genomes AF: 0.0101 AC: 1540 AN: 152168 Hom.: 9 Cov.: 33

Gnomad AFR AF: 0.00246

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.00779

Gnomad ASJ AF: 0.00606

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00517

Gnomad FIN AF: 0.00687

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0166

Gnomad OTH AF: 0.00956

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

GnomAD4 genome AF: 0.0101 AC: 1539 AN: 152286 Hom.: 9 Cov.: 33 AF XY: 0.00925 AC XY: 689 AN XY: 74458

Gnomad4 AFR AF: 0.00245

Gnomad4 AMR AF: 0.00778

Gnomad4 ASJ AF: 0.00606

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00518

Gnomad4 FIN AF: 0.00687

Gnomad4 NFE AF: 0.0166

Gnomad4 OTH AF: 0.00946

Alfa AF: 0.0156 Hom.: 17

Bravo AF: 0.0102

Asia WGS AF: 0.00346 AC: 12 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
Cadd	Benign	5.7
Dann	Benign	0.76

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: rs1641895; hg19: chr16-12641115;