Variant 9-112838568-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_001012994.2(SNX30):c.885T>C(p.Ala295=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.976 in 1,614,174 control chromosomes in the GnomAD database, including 768,448 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.98 ( 73794 hom., cov: 31)

Exomes 𝑓: 0.97 ( 694654 hom. )

Consequence

SNX30
NM_001012994.2 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -6.83

Variant links:

Genes affected

SNX30 (HGNC:23685): (sorting nexin family member 30) Predicted to enable phosphatidylinositol binding activity. Predicted to be involved in protein transport. [provided by Alliance of Genome Resources, Apr 2022]

SNX30 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP6

Variant 9-112838568-T-C is Benign according to our data. Variant chr9-112838568-T-C is described in ClinVar as [Benign]. Clinvar id is 1329645.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-6.83 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.987 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNX30	NM_001012994.2 linkuse as main transcript	c.885T>C	p.Ala295=	synonymous_variant	6/9	ENST00000374232.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNX30	ENST00000374232.8 linkuse as main transcript	c.885T>C	p.Ala295=	synonymous_variant	6/9	5	NM_001012994.2	P1
SNX30	ENST00000416585.1 linkuse as main transcript			upstream_gene_variant		3

Frequencies

GnomAD3 genomes

AF:

0.984

AC:

149793

AN:

152198

Hom.:

73736

Cov.:

show subpopulations

Gnomad AFR

AF:

0.995

Gnomad AMI

AF:

0.996

Gnomad AMR

AF:

0.992

Gnomad ASJ

AF:

0.999

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

0.994

Gnomad FIN

AF:

0.985

Gnomad MID

AF:

1.00

Gnomad NFE

AF:

0.973

Gnomad OTH

AF:

0.987

GnomAD3 exomes

AF:

0.983

AC:

245290

AN:

249534

Hom.:

120590

AF XY:

0.983

AC XY:

133032

AN XY:

135382

show subpopulations

Gnomad AFR exome

AF:

0.995

Gnomad AMR exome

AF:

0.995

Gnomad ASJ exome

AF:

0.997

Gnomad EAS exome

AF:

1.00

Gnomad SAS exome

AF:

0.994

Gnomad FIN exome

AF:

0.983

Gnomad NFE exome

AF:

0.971

Gnomad OTH exome

AF:

0.987

GnomAD4 exome

AF:

0.975

AC:

1425014

AN:

1461858

Hom.:

694654

Cov.:

AF XY:

0.976

AC XY:

709427

AN XY:

727234

show subpopulations

Gnomad4 AFR exome

AF:

0.996

Gnomad4 AMR exome

AF:

0.994

Gnomad4 ASJ exome

AF:

0.998

Gnomad4 EAS exome

AF:

1.00

Gnomad4 SAS exome

AF:

0.994

Gnomad4 FIN exome

AF:

0.982

Gnomad4 NFE exome

AF:

0.970

Gnomad4 OTH exome

AF:

0.979

GnomAD4 genome

AF:

0.984

AC:

149910

AN:

152316

Hom.:

73794

Cov.:

AF XY:

0.986

AC XY:

73416

AN XY:

74474

show subpopulations

Gnomad4 AFR

AF:

0.995

Gnomad4 AMR

AF:

0.992

Gnomad4 ASJ

AF:

0.999

Gnomad4 EAS

AF:

1.00

Gnomad4 SAS

AF:

0.994

Gnomad4 FIN

AF:

0.985

Gnomad4 NFE

AF:

0.973

Gnomad4 OTH

AF:

0.987

Alfa

AF:

0.978

Hom.:

36803

Bravo

AF:

0.985

Asia WGS

AF:

0.996

AC:

3463

AN:

3478

EpiCase

AF:

0.977

EpiControl

AF:

0.977

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Dec 23, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

Cadd

Benign

0.23

Dann

Benign

0.41

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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

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