Variant chr1-151612258-T-TGGC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2

The NM_001330723.2(SNX27):c.69_71dupCGG(p.Gly24dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00421 in 1,440,430 control chromosomes in the GnomAD database, including 16 homozygotes. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. G24G) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.0043 ( 2 hom., cov: 32)

Exomes 𝑓: 0.0042 ( 14 hom. )

Consequence

SNX27
NM_001330723.2 disruptive_inframe_insertion

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.07

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 Benign. Variant got -10 ACMG points.

BP6

Variant 1-151612258-T-TGGC is Benign according to our data. Variant chr1-151612258-T-TGGC is described in ClinVar as [Benign]. Clinvar id is 462816.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00425 (645/151608) while in subpopulation NFE AF= 0.00579 (393/67830). AF 95% confidence interval is 0.00532. There are 2 homozygotes in gnomad4. There are 345 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High AC in GnomAd4 at 645 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNX27	NM_001330723.2 link	c.69_71dupCGG	p.Gly24dup	disruptive_inframe_insertion	Exon 1 of 12	ENST00000458013.7	NP_001317652.1	Q96L92-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNX27	ENST00000458013.7 link	c.69_71dupCGG	p.Gly24dup	disruptive_inframe_insertion	Exon 1 of 12	5	NM_001330723.2	ENSP00000400333.2		Q96L92-1

Frequencies

GnomAD3 genomes

AF:

0.00426

AC:

645

AN:

151502

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000995

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000918

Gnomad ASJ

AF:

0.00260

Gnomad EAS

AF:

0.000389

Gnomad SAS

AF:

0.00125

Gnomad FIN

AF:

0.0169

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00579

Gnomad OTH

AF:

0.000960

GnomAD3 exomes

AF:

0.00373

AC:

178

AN:

47704

Hom.:

AF XY:

0.00342

AC XY:

AN XY:

27186

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.000743

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00109

Gnomad FIN exome

AF:

0.0120

Gnomad NFE exome

AF:

0.00301

Gnomad OTH exome

AF:

0.00600

GnomAD4 exome

AF:

0.00421

AC:

5420

AN:

1288822

Hom.:

Cov.:

AF XY:

0.00423

AC XY:

2675

AN XY:

632138

show subpopulations

Gnomad4 AFR exome

AF:

0.000537

Gnomad4 AMR exome

AF:

0.000966

Gnomad4 ASJ exome

AF:

0.00325

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00125

Gnomad4 FIN exome

AF:

0.0147

Gnomad4 NFE exome

AF:

0.00430

Gnomad4 OTH exome

AF:

0.00335

GnomAD4 genome

AF:

0.00425

AC:

645

AN:

151608

Hom.:

Cov.:

AF XY:

0.00466

AC XY:

345

AN XY:

74098

show subpopulations

Gnomad4 AFR

AF:

0.000992

Gnomad4 AMR

AF:

0.000917

Gnomad4 ASJ

AF:

0.00260

Gnomad4 EAS

AF:

0.000390

Gnomad4 SAS

AF:

0.00125

Gnomad4 FIN

AF:

0.0169

Gnomad4 NFE

AF:

0.00579

Gnomad4 OTH

AF:

0.000950

Bravo

AF:

0.00306

Asia WGS

AF:

0.000870

AC:

AN:

3462

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Severe myoclonic epilepsy in infancy

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Feb 02, 2025

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Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over