Variant chrX-85107555-T-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2

The NM_001367857.2(SATL1):c.1414A>T(p.Ser472Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000477 in 1,210,907 control chromosomes in the GnomAD database, including 2 homozygotes. There are 171 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.0025 ( 0 hom., 95 hem., cov: 24)

Exomes 𝑓: 0.00027 ( 2 hom. 76 hem. )

Consequence

SATL1
NM_001367857.2 missense

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.0850

Variant links:

Genes affected

SATL1 (HGNC:27992): (spermidine/spermine N1-acetyl transferase like 1) Predicted to enable N-acetyltransferase activity. [provided by Alliance of Genome Resources, Apr 2022]

SATL1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0038968325).

BP6

Variant X-85107555-T-A is Benign according to our data. Variant chrX-85107555-T-A is described in ClinVar as [Benign]. Clinvar id is 3049685.Status of the report is no_assertion_criteria_provided, 0 stars.

BS2

High Hemizygotes in GnomAd4 at 95 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
SATL1	NM_001367857.2 linkuse as main transcript	c.1414A>T	p.Ser472Cys	missense_variant	3/8	ENST00000644105.2
SATL1	NM_001367858.2 linkuse as main transcript	c.1414A>T	p.Ser472Cys	missense_variant	7/12
SATL1	NM_001012980.2 linkuse as main transcript	c.1414A>T	p.Ser472Cys	missense_variant	1/5
SATL1	XM_047442081.1 linkuse as main transcript	c.1414A>T	p.Ser472Cys	missense_variant	2/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SATL1	ENST00000644105.2 linkuse as main transcript	c.1414A>T	p.Ser472Cys	missense_variant	3/8		NM_001367857.2	A2	Q86VE3-1

Frequencies

GnomAD3 genomes

AF:

0.00253

AC:

285

AN:

112664

Hom.:

Cov.:

AF XY:

0.00276

AC XY:

AN XY:

34838

show subpopulations

Gnomad AFR

AF:

0.00861

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00103

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000363

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000375

Gnomad OTH

AF:

0.00263

GnomAD3 exomes

AF:

0.000644

AC:

118

AN:

183355

Hom.:

AF XY:

0.000472

AC XY:

AN XY:

67839

show subpopulations

Gnomad AFR exome

AF:

0.00813

Gnomad AMR exome

AF:

0.000292

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000367

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.000269

AC:

295

AN:

1098194

Hom.:

Cov.:

AF XY:

0.000209

AC XY:

AN XY:

363552

show subpopulations

Gnomad4 AFR exome

AF:

0.00864

Gnomad4 AMR exome

AF:

0.000483

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000344

Gnomad4 OTH exome

AF:

0.000434

GnomAD4 genome

AF:

0.00251

AC:

283

AN:

112713

Hom.:

Cov.:

AF XY:

0.00272

AC XY:

AN XY:

34897

show subpopulations

Gnomad4 AFR

AF:

0.00856

Gnomad4 AMR

AF:

0.00103

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000375

Gnomad4 OTH

AF:

0.00259

Alfa

AF:

0.00125

Hom.:

Bravo

AF:

0.00282

ESP6500AA

AF:

0.00678

AC:

ESP6500EA

AF:

0.00

AC:

ExAC

AF:

0.000725

AC:

EpiCase

AF:

0.000164

EpiControl

AF:

0.00

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

SATL1-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Jul 11, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.10

BayesDel_addAF

Benign

-0.64

BayesDel_noAF

Benign

-0.69

CADD

Benign

DANN

Uncertain

0.98

DEOGEN2

Benign

0.012

T;.;.;.;.

FATHMM_MKL

Benign

0.074

LIST_S2

Benign

0.45

.;T;T;.;T

M_CAP

Benign

0.0046

MetaRNN

Benign

0.0039

T;T;T;T;T

MetaSVM

Benign

-0.94

MutationAssessor

Uncertain

2.1

M;.;.;.;.

MutationTaster

Benign

1.0

N;N;N

PrimateAI

Benign

0.23

PROVEAN

Benign

-1.4

N;N;.;.;.

REVEL

Benign

0.071

Sift

Uncertain

0.0020

D;D;.;.;.

Sift4G

Uncertain

0.013

D;D;.;.;.

Polyphen

1.0

D;.;.;.;.

Vest4

0.059

MVP

0.21

MPC

0.35

ClinPred

0.027

GERP RS

3.5

Varity_R

0.20

gMVP

0.13

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