Variant rs567208173 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_001330723.2(SNX27):c.69_71delCGG(p.Gly24del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.0000668 in 1,288,054 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. G23G) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.000067 ( 0 hom. )

Consequence

SNX27
NM_001330723.2 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.89

Variant links:

Genes affected

SNX27 (HGNC:20073): (sorting nexin 27) This gene encodes a member of the sorting nexin family, a diverse group of cytoplasmic and membrane-associated proteins involved in endocytosis of plasma membrane receptors and protein trafficking through these compartments. All members of this protein family contain a phosphoinositide binding domain (PX domain). A highly similar protein in mouse is responsible for the specific recruitment of an isoform of serotonin 5-hydroxytryptamine 4 receptor into early endosomes, suggesting the analogous role for the human protein. [provided by RefSeq, Jul 2008]

SNX27 links:

ENSG00000250734 (HGNC:):

ENSG00000250734 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS2

High AC in GnomAdExome4 at 86 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SNX27	NM_001330723.2 linkuse as main transcript	c.69_71delCGG	p.Gly24del	disruptive_inframe_deletion	1/12	ENST00000458013.7	NP_001317652.1	Q96L92-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SNX27	ENST00000458013.7 linkuse as main transcript	c.69_71delCGG	p.Gly24del	disruptive_inframe_deletion	1/12	5	NM_001330723.2	ENSP00000400333.2		Q96L92-1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.000943

AC:

AN:

47704

Hom.:

AF XY:

0.00103

AC XY:

AN XY:

27186

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00119

Gnomad ASJ exome

AF:

0.000394

Gnomad EAS exome

AF:

0.000519

Gnomad SAS exome

AF:

0.00133

Gnomad FIN exome

AF:

0.000563

Gnomad NFE exome

AF:

0.00109

Gnomad OTH exome

AF:

0.000858

GnomAD4 exome

AF:

0.0000668

AC:

AN:

1288054

Hom.:

AF XY:

0.0000760

AC XY:

AN XY:

631698

show subpopulations

Gnomad4 AFR exome

AF:

0.0000384

Gnomad4 AMR exome

AF:

0.000512

Gnomad4 ASJ exome

AF:

0.0000508

Gnomad4 EAS exome

AF:

0.0000696

Gnomad4 SAS exome

AF:

0.000340

Gnomad4 FIN exome

AF:

0.000142

Gnomad4 NFE exome

AF:

0.0000398

Gnomad4 OTH exome

AF:

0.0000754

GnomAD4 genome

Cov.:

Bravo

AF:

0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing