Variant 7-117222922-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PP2BP4_StrongBP6_ModerateBS2

The ENST00000265437.9(ST7):c.1700G>T(p.Arg567Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00959 in 1,614,050 control chromosomes in the GnomAD database, including 106 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R567C) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.0073 ( 13 hom., cov: 32)

Exomes 𝑓: 0.0098 ( 93 hom. )

Consequence

ST7
ENST00000265437.9 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.237

Variant links:

Genes affected

ST7 (HGNC:11351): (suppression of tumorigenicity 7) The gene for this product maps to a region on chromosome 7 identified as an autism-susceptibility locus. Mutation screening of the entire coding region in autistic individuals failed to identify phenotype-specific variants, suggesting that coding mutations for this gene are unlikely to be involved in the etiology of autism. The function of this gene product has not been determined. Transcript variants encoding different isoforms of this protein have been described. [provided by RefSeq, Jul 2008]

ST7 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

PP2

Missense variant where missense usually causes diseases, ST7

BP4

Computational evidence support a benign effect (MetaRNN=0.0031498969).

BP6

Variant 7-117222922-G-T is Benign according to our data. Variant chr7-117222922-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 774316.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High AC in GnomAd at 1106 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ST7	NM_001369598.1 linkuse as main transcript	c.1638+860G>T		intron_variant		ENST00000323984.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ST7	ENST00000323984.8 linkuse as main transcript	c.1638+860G>T		intron_variant		5	NM_001369598.1

Frequencies

GnomAD3 genomes

AF:

0.00727

AC:

1106

AN:

152092

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00239

Gnomad AMI

AF:

0.00329

Gnomad AMR

AF:

0.0148

Gnomad ASJ

AF:

0.00605

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.00145

Gnomad FIN

AF:

0.00292

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0102

Gnomad OTH

AF:

0.0101

GnomAD3 exomes

AF:

0.00657

AC:

1637

AN:

249034

Hom.:

AF XY:

0.00681

AC XY:

918

AN XY:

134808

show subpopulations

Gnomad AFR exome

AF:

0.00215

Gnomad AMR exome

AF:

0.00708

Gnomad ASJ exome

AF:

0.00357

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00252

Gnomad FIN exome

AF:

0.00370

Gnomad NFE exome

AF:

0.0101

Gnomad OTH exome

AF:

0.00735

GnomAD4 exome

AF:

0.00983

AC:

14367

AN:

1461840

Hom.:

Cov.:

AF XY:

0.00957

AC XY:

6960

AN XY:

727226

show subpopulations

Gnomad4 AFR exome

AF:

0.00284

Gnomad4 AMR exome

AF:

0.00749

Gnomad4 ASJ exome

AF:

0.00367

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00264

Gnomad4 FIN exome

AF:

0.00346

Gnomad4 NFE exome

AF:

0.0116

Gnomad4 OTH exome

AF:

0.00785

GnomAD4 genome

AF:

0.00727

AC:

1106

AN:

152210

Hom.:

Cov.:

AF XY:

0.00709

AC XY:

528

AN XY:

74422

show subpopulations

Gnomad4 AFR

AF:

0.00238

Gnomad4 AMR

AF:

0.0148

Gnomad4 ASJ

AF:

0.00605

Gnomad4 EAS

AF:

0.000386

Gnomad4 SAS

AF:

0.00145

Gnomad4 FIN

AF:

0.00292

Gnomad4 NFE

AF:

0.0102

Gnomad4 OTH

AF:

0.00996

Alfa

AF:

0.00890

Hom.:

Bravo

AF:

0.00797

TwinsUK

AF:

0.0129

AC:

ALSPAC

AF:

0.0158

AC:

ESP6500AA

AF:

0.000908

AC:

ESP6500EA

AF:

0.0110

AC:

ExAC

AF:

0.00596

AC:

723

Asia WGS

AF:

0.000866

AC:

AN:

3478

EpiCase

AF:

0.0104

EpiControl

AF:

0.0107

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Invitae

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.11

BayesDel_addAF

Benign

-0.62

BayesDel_noAF

Benign

-0.65

Cadd

Benign

0.47

Dann

Uncertain

0.98

DEOGEN2

Benign

0.013

Eigen

Benign

-1.1

Eigen_PC

Benign

-1.1

FATHMM_MKL

Benign

0.025

LIST_S2

Benign

0.78

MetaRNN

Benign

0.0031

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.0

MutationTaster

Benign

1.0

N;N;N;N;N;N;N;N;N

PrimateAI

Benign

0.29

PROVEAN

Benign

0.36

REVEL

Benign

0.025

Sift

Benign

0.054

Sift4G

Uncertain

0.048

Polyphen

0.0

Vest4

0.14

MVP

0.043

MPC

1.1

ClinPred

0.0034

GERP RS

0.35

Varity_R

0.041

gMVP

0.34

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