chr16-12251327-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_032167.5(SNX29):​c.1679-26606T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.652 in 152,124 control chromosomes in the GnomAD database, including 33,438 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 0.65 ( 33438 hom., cov: 33)

Consequence

SNX29
NM_032167.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.140
Variant links:
Genes affected
SNX29 (HGNC:30542): (sorting nexin 29) Predicted to enable phosphatidylinositol binding activity. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SNX29NM_032167.5 linkc.1679-26606T>G intron_variant Intron 14 of 20 ENST00000566228.6 NP_115543.3 Q8TEQ0-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SNX29ENST00000566228.6 linkc.1679-26606T>G intron_variant Intron 14 of 20 5 NM_032167.5 ENSP00000456480.1 Q8TEQ0-1
SNX29ENST00000564791.5 linkc.146-26606T>G intron_variant Intron 2 of 8 1 ENSP00000457017.1 A0A0C4DGM3

Frequencies

GnomAD3 genomes
AF:
0.652
AC:
99158
AN:
152006
Hom.:
33384
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.821
Gnomad AMI
AF:
0.563
Gnomad AMR
AF:
0.610
Gnomad ASJ
AF:
0.641
Gnomad EAS
AF:
0.631
Gnomad SAS
AF:
0.335
Gnomad FIN
AF:
0.495
Gnomad MID
AF:
0.601
Gnomad NFE
AF:
0.611
Gnomad OTH
AF:
0.598
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.652
AC:
99254
AN:
152124
Hom.:
33438
Cov.:
33
AF XY:
0.640
AC XY:
47578
AN XY:
74354
show subpopulations
African (AFR)
AF:
0.821
AC:
34096
AN:
41516
American (AMR)
AF:
0.609
AC:
9321
AN:
15294
Ashkenazi Jewish (ASJ)
AF:
0.641
AC:
2225
AN:
3470
East Asian (EAS)
AF:
0.631
AC:
3256
AN:
5158
South Asian (SAS)
AF:
0.335
AC:
1617
AN:
4824
European-Finnish (FIN)
AF:
0.495
AC:
5231
AN:
10566
Middle Eastern (MID)
AF:
0.616
AC:
181
AN:
294
European-Non Finnish (NFE)
AF:
0.611
AC:
41570
AN:
67986
Other (OTH)
AF:
0.591
AC:
1245
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1710
3420
5130
6840
8550
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
770
1540
2310
3080
3850
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.621
Hom.:
57404
Bravo
AF:
0.672
Asia WGS
AF:
0.461
AC:
1603
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
1.2
DANN
Benign
0.30
PhyloP100
-0.14
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

Publications

Other links and lift over

dbSNP: rs7195058; hg19: chr16-12345184; API