Variant chr1-112616842-T-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The NM_017744.5(ST7L):c.259A>T(p.Thr87Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00883 in 1,606,180 control chromosomes in the GnomAD database, including 96 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0067 ( 9 hom., cov: 32)

Exomes 𝑓: 0.0091 ( 87 hom. )

Consequence

ST7L
NM_017744.5 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 7.90

Variant links:

Genes affected

ST7L (HGNC:18441): (suppression of tumorigenicity 7 like) This gene was identified by its similarity to the ST7 tumor suppressor gene found in the chromosome 7q31 region. This gene is clustered in a tail-to-tail manner with the WNT2B gene in a chromosomal region known to be deleted and rearranged in a variety of cancers. Several transcript variants encoding many different isoforms have been described, but some have not been fully characterized. [provided by RefSeq, Feb 2011]

ST7L links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP6

Variant 1-112616842-T-A is Benign according to our data. Variant chr1-112616842-T-A is described in ClinVar as [Benign]. Clinvar id is 790336.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 9 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ST7L	NM_017744.5 linkuse as main transcript	c.259A>T	p.Thr87Ser	missense_variant	2/15	ENST00000358039.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ST7L	ENST00000358039.9 linkuse as main transcript	c.259A>T	p.Thr87Ser	missense_variant	2/15	1	NM_017744.5		Q8TDW4-1

Frequencies

GnomAD3 genomes

AF:

0.00671

AC:

1020

AN:

151958

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00155

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.00656

Gnomad ASJ

AF:

0.00923

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00166

Gnomad FIN

AF:

0.0111

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0100

Gnomad OTH

AF:

0.00768

GnomAD3 exomes

AF:

0.00664

AC:

1632

AN:

245942

Hom.:

AF XY:

0.00652

AC XY:

866

AN XY:

132868

show subpopulations

Gnomad AFR exome

AF:

0.00118

Gnomad AMR exome

AF:

0.00457

Gnomad ASJ exome

AF:

0.00992

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00244

Gnomad FIN exome

AF:

0.0125

Gnomad NFE exome

AF:

0.00874

Gnomad OTH exome

AF:

0.00694

GnomAD4 exome

AF:

0.00905

AC:

13161

AN:

1454102

Hom.:

Cov.:

AF XY:

0.00892

AC XY:

6454

AN XY:

723224

show subpopulations

Gnomad4 AFR exome

AF:

0.00136

Gnomad4 AMR exome

AF:

0.00456

Gnomad4 ASJ exome

AF:

0.0101

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00279

Gnomad4 FIN exome

AF:

0.0125

Gnomad4 NFE exome

AF:

0.0101

Gnomad4 OTH exome

AF:

0.00920

GnomAD4 genome

AF:

0.00671

AC:

1020

AN:

152078

Hom.:

Cov.:

AF XY:

0.00702

AC XY:

522

AN XY:

74340

show subpopulations

Gnomad4 AFR

AF:

0.00154

Gnomad4 AMR

AF:

0.00655

Gnomad4 ASJ

AF:

0.00923

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00166

Gnomad4 FIN

AF:

0.0111

Gnomad4 NFE

AF:

0.0100

Gnomad4 OTH

AF:

0.00760

Alfa

AF:

0.00900

Hom.:

Bravo

AF:

0.00645

TwinsUK

AF:

0.0108

AC:

ALSPAC

AF:

0.00986

AC:

ESP6500AA

AF:

0.00159

AC:

ESP6500EA

AF:

0.00930

AC:

ExAC

AF:

0.00631

AC:

766

Asia WGS

AF:

0.000289

AC:

AN:

3478

EpiCase

AF:

0.00912

EpiControl

AF:

0.00938

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

Invitae

Jul 19, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.59

BayesDel_addAF

Benign

-0.31

BayesDel_noAF

Benign

-0.21

CADD

Pathogenic

DANN

Uncertain

1.0

Eigen

Pathogenic

0.86

Eigen_PC

Pathogenic

0.84

FATHMM_MKL

Pathogenic

0.98

LIST_S2

Pathogenic

0.99

D;D;D;D;D;D

MetaRNN

Benign

0.015

T;T;T;T;T;T

MetaSVM

Benign

-0.77

MutationAssessor

Uncertain

2.9

M;M;.;M;.;.

MutationTaster

Benign

1.0

D;D;D;D;D;D;D;D;D;D

PrimateAI

Uncertain

0.57

PROVEAN

Uncertain

-3.0

D;D;D;D;D;D

REVEL

Uncertain

0.49

Sift

Uncertain

0.0030

D;D;D;D;D;D

Sift4G

Uncertain

0.011

D;D;D;D;D;.

Polyphen

1.0

D;D;D;D;D;.

Vest4

0.76

MutPred

0.82

Gain of sheet (P = 0.0827);Gain of sheet (P = 0.0827);.;Gain of sheet (P = 0.0827);.;.;

MVP

0.69

MPC

0.39

ClinPred

0.017

GERP RS

6.0

Varity_R

0.51

gMVP

0.73

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.31

Details are displayed if max score is > 0.2

DS_DL_spliceai

0.31

Position offset: -29

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