1-98733890-T-C

Variant summary

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

The NM_015976.5(SNX7):c.1126-4347T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 152,050 control chromosomes in the GnomAD database, including 6,133 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 0.28 (6133 hom., cov: 32)
• Consequence: SNX7 NM_015976.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.907

Genes affected

SNX7 (HGNC:14971): (sorting nexin 7) This gene encodes a member of the sorting nexin family. Members of this family contain a phox (PX) domain, which is a phosphoinositide binding domain, and are involved in intracellular trafficking. This protein does not contain a coiled coil region like some family members, and its exact function is unknown. Alternative splicing results in multiple transcript variants. A related pseudogene has been identified on chromosome 11. [provided by RefSeq, Jun 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.295 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNX7	NM_015976.5	c.1126-4347T>C		intron_variant		ENST00000306121.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNX7	ENST00000306121.8	c.1126-4347T>C		intron_variant		1	NM_015976.5	P1
SNX7	ENST00000528824.1	c.*946-26164T>C		intron_variant, NMD_transcript_variant		1
SNX7	ENST00000529992.5	c.961-4347T>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41994 AN: 151932 Hom.: 6123 Cov.: 32

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.0581

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.276 AC: 42035 AN: 152050 Hom.: 6133 Cov.: 32 AF XY: 0.275 AC XY: 20476 AN XY: 74364

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.0577

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.294

Gnomad4 OTH AF: 0.265

Alfa AF: 0.171 Hom.: 365

Bravo AF: 0.274

Asia WGS AF: 0.176 AC: 615 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.0
Dann	Benign	0.53

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: rs12057921; hg19: chr1-99199446;