rs3803602

Variant names:

• chr16-12571104-G-A
• rs3803602
• NM_032167.5:c.*2475G>A

Your query was ambiguous. Multiple possible variants found:

• chr16-12571104-G-A
• chr16-12571104-G-C
• chr16-12571104-G-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.*2475G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0247 in 232,550 control chromosomes in the GnomAD database, including 471 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as (no stars).

• Frequency:
  • Genomes: 𝑓 0.022 (281 hom., cov: 33)
  • Exomes 𝑓: 0.029 (190 hom.)
• Consequence: SNX29 NM_032167.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.290
• 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]

ENSG00000259899 (HGNC:58619):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.187 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNX29	NM_032167.5	MANE Select	c.*2475G>A		3_prime_UTR	Exon 21 of 21	NP_115543.3	Q8TEQ0-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNX29	ENST00000566228.6	TSL:5 MANE Select	c.*2475G>A		3_prime_UTR	Exon 21 of 21	ENSP00000456480.1	Q8TEQ0-1
	ENSG00000259899	ENST00000564505.2	TSL:3	n.347-9958C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0223 AC: 3392 AN: 152154 Hom.: 280 Cov.: 33

Gnomad AFR AF: 0.00468

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.000576

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.0513

Gnomad FIN AF: 0.0103

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00151

Gnomad OTH AF: 0.0244

GnomAD4 exome AF: 0.0294 AC: 2359 AN: 80278 Hom.: 190 Cov.: 0 AF XY: 0.0269 AC XY: 994 AN XY: 36906

African (AFR) AF: 0.00388 AC: 15 AN: 3866

American (AMR) AF: 0.141 AC: 347 AN: 2466

Ashkenazi Jewish (ASJ) AF: 0.00118 AC: 6 AN: 5080

East Asian (EAS) AF: 0.155 AC: 1752 AN: 11308

South Asian (SAS) AF: 0.0460 AC: 32 AN: 696

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 60

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 494

European-Non Finnish (NFE) AF: 0.00107 AC: 53 AN: 49604

Other (OTH) AF: 0.0230 AC: 154 AN: 6704

GnomAD4 genome AF: 0.0223 AC: 3393 AN: 152272 Hom.: 281 Cov.: 33 AF XY: 0.0256 AC XY: 1906 AN XY: 74458

African (AFR) AF: 0.00467 AC: 194 AN: 41562

American (AMR) AF: 0.109 AC: 1668 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.000576 AC: 2 AN: 3472

East Asian (EAS) AF: 0.197 AC: 1017 AN: 5174

South Asian (SAS) AF: 0.0514 AC: 248 AN: 4828

European-Finnish (FIN) AF: 0.0103 AC: 109 AN: 10608

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00151 AC: 103 AN: 68016

Other (OTH) AF: 0.0247 AC: 52 AN: 2108

Alfa AF: 0.0128 Hom.: 459

Bravo AF: 0.0336

Asia WGS AF: 0.119 AC: 411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.0
DANN	Benign	0.57
PhyloP100		0.29
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: rs3803602; hg19: chr16-12664961;