7-2306480-C-T

Variant names:

• chr7-2306480-C-T
• rs10249052
• NM_013321.4:c.94+7848G>A

Variant summary

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

The NM_013321.4(SNX8):​c.94+7848G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.365 in 151,936 control chromosomes in the GnomAD database, including 10,466 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 0.36 (10466 hom., cov: 32)
• Consequence: SNX8 NM_013321.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 3 publications found

Genes affected

SNX8 (HGNC:14972): (sorting nexin 8) Enables identical protein binding activity and phosphatidylinositol binding activity. Involved in early endosome to Golgi transport and intracellular protein transport. Located in early endosome membrane. Colocalizes with retromer complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.575 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_013321.4. 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
	SNX8	NM_013321.4	MANE Select	c.94+7848G>A		intron	N/A	NP_037453.1	Q9Y5X2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNX8	ENST00000222990.8	TSL:1 MANE Select	c.94+7848G>A		intron	N/A	ENSP00000222990.3	Q9Y5X2
	SNX8	ENST00000926983.1		c.94+7848G>A		intron	N/A	ENSP00000597042.1
	SNX8	ENST00000878404.1		c.94+7848G>A		intron	N/A	ENSP00000548463.1

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55373 AN: 151818 Hom.: 10437 Cov.: 32

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.365 AC: 55449 AN: 151936 Hom.: 10466 Cov.: 32 AF XY: 0.368 AC XY: 27356 AN XY: 74260

African (AFR) AF: 0.384 AC: 15890 AN: 41410

American (AMR) AF: 0.432 AC: 6587 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 960 AN: 3470

East Asian (EAS) AF: 0.592 AC: 3057 AN: 5160

South Asian (SAS) AF: 0.384 AC: 1851 AN: 4820

European-Finnish (FIN) AF: 0.285 AC: 3008 AN: 10560

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.339 AC: 23031 AN: 67962

Other (OTH) AF: 0.359 AC: 759 AN: 2112

Alfa AF: 0.350 Hom.: 12180

Bravo AF: 0.378

Asia WGS AF: 0.536 AC: 1860 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.89
DANN	Benign	0.60
PhyloP100		-1.1
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: rs10249052; hg19: chr7-2346115;