6-157748231-G-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 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=-0.91).
• 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

African (AFR) AF: 0.941 AC: 39073 AN: 41544

American (AMR) AF: 0.820 AC: 12532 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.741 AC: 2573 AN: 3472

East Asian (EAS) AF: 0.687 AC: 3557 AN: 5178

South Asian (SAS) AF: 0.814 AC: 3912 AN: 4806

European-Finnish (FIN) AF: 0.722 AC: 7615 AN: 10554

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.737 AC: 50091 AN: 67984

Other (OTH) AF: 0.762 AC: 1613 AN: 2116

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
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs684340; hg19: chr6-158169263;