16-12269178-C-T

Variant names:

• chr16-12269178-C-T
• rs7191435
• NM_032167.5:c.1679-8755C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.854 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032167.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNX29	NM_032167.5	MANE Select	c.1679-8755C>T		intron	N/A	NP_115543.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNX29	ENST00000566228.6	TSL:5 MANE Select	c.1679-8755C>T		intron	N/A	ENSP00000456480.1
	SNX29	ENST00000564791.5	TSL:1	c.146-8755C>T		intron	N/A	ENSP00000457017.1

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

African (AFR) AF: 0.861 AC: 35775 AN: 41534

American (AMR) AF: 0.648 AC: 9909 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.736 AC: 2557 AN: 3472

East Asian (EAS) AF: 0.786 AC: 4070 AN: 5180

South Asian (SAS) AF: 0.422 AC: 2036 AN: 4824

European-Finnish (FIN) AF: 0.519 AC: 5493 AN: 10576

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.649 AC: 44115 AN: 67984

Other (OTH) AF: 0.645 AC: 1362 AN: 2110

Alfa AF: 0.672 Hom.: 107498

Bravo AF: 0.718

Asia WGS AF: 0.616 AC: 2141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.10
DANN	Benign	0.49
PhyloP100		-2.0
Mutation Taster		=100/0	polymorphism (auto)

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: rs7191435; hg19: chr16-12363035;