dbSNP rs2019213: SNX7:p.Glu432Glu (chr1-98760071-G-A) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_015976.5(SNX7):c.1296G>A(p.Glu432Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.967 in 1,605,966 control chromosomes in the GnomAD database, including 753,696 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 0.94 ( 67798 hom., cov: 31)

Exomes 𝑓: 0.97 ( 685898 hom. )

Consequence

SNX7
NM_015976.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00400

Variant links:

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]

SNX7 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.58).

BP7

Synonymous conserved (PhyloP=0.004 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.981 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNX7	NM_015976.5 link	c.1296G>A	p.Glu432Glu	synonymous_variant	Exon 9 of 9	ENST00000306121.8	NP_057060.2	Q9UNH6-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
SNX7	ENST00000306121.8 link	c.1296G>A	p.Glu432Glu	synonymous_variant	Exon 9 of 9	1	NM_015976.5	ENSP00000304429.3	Q9UNH6-3
SNX7	ENST00000528824.1 link	n.*963G>A		non_coding_transcript_exon_variant	Exon 9 of 9	1		ENSP00000435172.1	E9PLE1
SNX7	ENST00000528824.1 link	n.*963G>A		3_prime_UTR_variant	Exon 9 of 9	1		ENSP00000435172.1	E9PLE1
SNX7	ENST00000529992.5 link	c.1131G>A	p.Glu377Glu	synonymous_variant	Exon 8 of 8	2		ENSP00000434731.1	E9PNL2

Frequencies

GnomAD3 genomes

AF:

0.942

AC:

143137

AN:

151964

Hom.:

67774

Cov.:

show subpopulations

Gnomad AFR

AF:

0.897

Gnomad AMI

AF:

0.968

Gnomad AMR

AF:

0.919

Gnomad ASJ

AF:

0.989

Gnomad EAS

AF:

0.658

Gnomad SAS

AF:

0.955

Gnomad FIN

AF:

0.971

Gnomad MID

AF:

0.978

Gnomad NFE

AF:

0.987

Gnomad OTH

AF:

0.951

GnomAD3 exomes

AF:

0.934

AC:

233974

AN:

250536

Hom.:

110424

AF XY:

0.942

AC XY:

127616

AN XY:

135448

show subpopulations

Gnomad AFR exome

AF:

0.895

Gnomad AMR exome

AF:

0.850

Gnomad ASJ exome

AF:

0.989

Gnomad EAS exome

AF:

0.651

Gnomad SAS exome

AF:

0.972

Gnomad FIN exome

AF:

0.973

Gnomad NFE exome

AF:

0.987

Gnomad OTH exome

AF:

0.957

GnomAD4 exome

AF:

0.969

AC:

1409254

AN:

1453884

Hom.:

685898

Cov.:

AF XY:

0.970

AC XY:

702226

AN XY:

723768

show subpopulations

Gnomad4 AFR exome

AF:

0.893

Gnomad4 AMR exome

AF:

0.857

Gnomad4 ASJ exome

AF:

0.988

Gnomad4 EAS exome

AF:

0.645

Gnomad4 SAS exome

AF:

0.971

Gnomad4 FIN exome

AF:

0.974

Gnomad4 NFE exome

AF:

0.987

Gnomad4 OTH exome

AF:

0.961

GnomAD4 genome

AF:

0.942

AC:

143216

AN:

152082

Hom.:

67798

Cov.:

AF XY:

0.939

AC XY:

69767

AN XY:

74332

show subpopulations

Gnomad4 AFR

AF:

0.897

Gnomad4 AMR

AF:

0.918

Gnomad4 ASJ

AF:

0.989

Gnomad4 EAS

AF:

0.658

Gnomad4 SAS

AF:

0.954

Gnomad4 FIN

AF:

0.971

Gnomad4 NFE

AF:

0.987

Gnomad4 OTH

AF:

0.950

Alfa

AF:

0.971

Hom.:

152328

Bravo

AF:

0.931

Asia WGS

AF:

0.831

AC:

2891

AN:

3476

EpiCase

AF:

0.986

EpiControl

AF:

0.987

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.58

CADD

Benign

3.4

DANN

Benign

0.46

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over