6-157776137-A-T

Variant names:

• chr6-157776137-A-T
• rs2770112
• ENST00000614703.4:c.-53-3687A>T

Variant summary

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

The ENST00000614703.4(SNX9):​c.-53-3687A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.567 in 152,054 control chromosomes in the GnomAD database, including 24,912 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 0.57 (24912 hom., cov: 32)
• Consequence: SNX9 ENST00000614703.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.752
• Publications: 3 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000614703.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNX9	ENST00000614703.4	TSL:4	c.-53-3687A>T		intron	N/A	ENSP00000482920.1
	SNX9	ENST00000614800.4	TSL:4	c.-53-3687A>T		intron	N/A	ENSP00000479382.1

Frequencies

GnomAD3 genomes AF: 0.566 AC: 86060 AN: 151936 Hom.: 24886 Cov.: 32

Gnomad AFR AF: 0.676

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.581

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.567 AC: 86140 AN: 152054 Hom.: 24912 Cov.: 32 AF XY: 0.571 AC XY: 42456 AN XY: 74294

African (AFR) AF: 0.676 AC: 28034 AN: 41492

American (AMR) AF: 0.587 AC: 8974 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.563 AC: 1953 AN: 3470

East Asian (EAS) AF: 0.497 AC: 2567 AN: 5166

South Asian (SAS) AF: 0.636 AC: 3066 AN: 4818

European-Finnish (FIN) AF: 0.581 AC: 6132 AN: 10554

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.495 AC: 33642 AN: 67956

Other (OTH) AF: 0.519 AC: 1096 AN: 2110

Alfa AF: 0.534 Hom.: 2739

Bravo AF: 0.567

Asia WGS AF: 0.614 AC: 2131 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.69
DANN	Benign	0.52
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs2770112; hg19: chr6-158197169;