1-151612258-TGGC-T

Position:

• chr1-151612258-TGGC-T

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.89

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]

ENSG00000250734 (HGNC:):

ACMG classification

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	c.69_71delCGG	p.Gly24del	disruptive_inframe_deletion	1/12	ENST00000458013.7	NP_001317652.1

Ensembl

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

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD3 exomes AF: 0.000943 AC: 45 AN: 47704 Hom.: 0 AF XY: 0.00103 AC XY: 28 AN XY: 27186

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: 86 AN: 1288054 Hom.: 0 AF XY: 0.0000760 AC XY: 48 AN XY: 631698

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.: 32

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs567208173; hg19: chr1-151584734;