7-2301420-C-T

Position:

• chr7-2301420-C-T

Variant summary

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

The NM_013321.4(SNX8):​c.94+12908G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 152,130 control chromosomes in the GnomAD database, including 8,204 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 0.31 (8204 hom., cov: 32)
• Consequence: SNX8 NM_013321.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.282

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNX8	NM_013321.4	c.94+12908G>A		intron_variant		ENST00000222990.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNX8	ENST00000222990.8	c.94+12908G>A		intron_variant		1	NM_013321.4	P1

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46428 AN: 152010 Hom.: 8198 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.594

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.226

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.305 AC: 46447 AN: 152130 Hom.: 8204 Cov.: 32 AF XY: 0.307 AC XY: 22803 AN XY: 74374

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.284

Gnomad4 EAS AF: 0.595

Gnomad4 SAS AF: 0.310

Gnomad4 FIN AF: 0.301

Gnomad4 NFE AF: 0.368

Gnomad4 OTH AF: 0.320

Alfa AF: 0.332 Hom.: 1507

Bravo AF: 0.310

Asia WGS AF: 0.457 AC: 1586 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	6.8
DANN	Benign	0.86

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

Publications

LitVar

Other links and lift over

dbSNP: rs13245097; hg19: chr7-2341055; COSMIC: COSV56127696; COSMIC: COSV56127696;