rs9355434

Variant names:

• chr6-157925231-A-G
• rs9355434
• NM_016224.5:c.1081-1880A>G

Your query was ambiguous. Multiple possible variants found:

• chr6-157925231-A-G
• chr6-157925231-A-T

Variant summary

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

The NM_016224.5(SNX9):​c.1081-1880A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 152,132 control chromosomes in the GnomAD database, including 3,625 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 0.22 (3625 hom., cov: 32)
• Consequence: SNX9 NM_016224.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.405
• Publications: 0 publications found

Genes affected

SNX9 (HGNC:14973): (sorting nexin 9) This gene encodes a member of the sorting nexin family. Members of this family contain a phosphoinositide binding domain, and are involved in intracellular trafficking. The encoded protein does not contain a coiled coil region, like some family members, but does contain a SRC homology domain near its N-terminus. The encoded protein is reported to have a variety of interaction partners, including of adaptor protein 2 , dynamin, tyrosine kinase non-receptor 2, Wiskott-Aldrich syndrome-like, and ARP3 actin-related protein 3. The encoded protein is implicated in several stages of intracellular trafficking, including endocytosis, macropinocytosis, and F-actin nucleation. [provided by RefSeq, Jul 2013]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.227 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNX9	NM_016224.5	c.1081-1880A>G		intron_variant	Intron 10 of 17	ENST00000392185.8	NP_057308.1
SNX9	XM_011535886.4	c.799-1880A>G		intron_variant	Intron 7 of 14		XP_011534188.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNX9	ENST00000392185.8	c.1081-1880A>G		intron_variant	Intron 10 of 17	1	NM_016224.5	ENSP00000376024.3

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32866 AN: 152014 Hom.: 3613 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.216 AC: 32916 AN: 152132 Hom.: 3625 Cov.: 32 AF XY: 0.215 AC XY: 16022 AN XY: 74356

African (AFR) AF: 0.226 AC: 9378 AN: 41488

American (AMR) AF: 0.163 AC: 2486 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 830 AN: 3472

East Asian (EAS) AF: 0.112 AC: 583 AN: 5190

South Asian (SAS) AF: 0.227 AC: 1092 AN: 4820

European-Finnish (FIN) AF: 0.214 AC: 2259 AN: 10580

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15667 AN: 67966

Other (OTH) AF: 0.214 AC: 453 AN: 2114

Alfa AF: 0.216 Hom.: 477

Bravo AF: 0.210

Asia WGS AF: 0.165 AC: 572 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.84
DANN	Benign	0.61
PhyloP100		-0.41
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: rs9355434; hg19: chr6-158346263;