rs684340

Variant names:

• chr6-157748231-G-A
• rs684340
• ENST00000614703.4:c.-205-18154G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-157748231-G-A
• chr6-157748231-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000614703.4(SNX9):​c.-205-18154G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.801 in 152,132 control chromosomes in the GnomAD database, including 49,472 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 0.80 (49472 hom., cov: 32)
• Consequence: SNX9 ENST00000614703.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.320

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.933 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNX9	ENST00000614703.4	c.-205-18154G>A		intron_variant	Intron 1 of 5	4		ENSP00000482920.1
SNX9	ENST00000614800.4	c.-205-18154G>A		intron_variant	Intron 1 of 5	4		ENSP00000479382.1

Frequencies

GnomAD3 genomes AF: 0.801 AC: 121791 AN: 152014 Hom.: 49414 Cov.: 32

Gnomad AFR AF: 0.940

Gnomad AMI AF: 0.790

Gnomad AMR AF: 0.820

Gnomad ASJ AF: 0.741

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.814

Gnomad FIN AF: 0.722

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.737

Gnomad OTH AF: 0.762

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

GnomAD4 genome AF: 0.801 AC: 121905 AN: 152132 Hom.: 49472 Cov.: 32 AF XY: 0.801 AC XY: 59584 AN XY: 74346

Gnomad4 AFR AF: 0.941

Gnomad4 AMR AF: 0.820

Gnomad4 ASJ AF: 0.741

Gnomad4 EAS AF: 0.687

Gnomad4 SAS AF: 0.814

Gnomad4 FIN AF: 0.722

Gnomad4 NFE AF: 0.737

Gnomad4 OTH AF: 0.762

Alfa AF: 0.761 Hom.: 5553

Bravo AF: 0.814

Asia WGS AF: 0.783 AC: 2716 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.29
DANN	Benign	0.39

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs684340; hg19: chr6-158169263;