Genetic Variant SATL1:p.Gln588* (chrX-85094928-G-A) – ACMG Classification: Likely_benign (-5 pts)

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2

The NM_001367857.2(SATL1):c.1762C>T(p.Gln588*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000279 in 1,175,949 control chromosomes in the GnomAD database, including 2 homozygotes. There are 190 hemizygotes in GnomAD. Variant has been reported in ClinVar as Likely benign (no stars). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: 𝑓 0.00012 ( 0 hom., 8 hem., cov: 23)

Exomes 𝑓: 0.00030 ( 2 hom. 182 hem. )

Consequence

SATL1
NM_001367857.2 stop_gained

Scores

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.00400

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 Likely_benign. Variant got -5 ACMG points.

BP6

Variant X-85094928-G-A is Benign according to our data. Variant chrX-85094928-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3042534.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-85094928-G-A is described in Lovd as [Likely_benign].

BS2

High Hemizygotes in GnomAd4 at 8 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SATL1	NM_001367857.2 link	c.1762C>T	p.Gln588*	stop_gained	Exon 5 of 8	ENST00000644105.2	NP_001354786.1
SATL1	NM_001367858.2 link	c.1762C>T	p.Gln588*	stop_gained	Exon 9 of 12		NP_001354787.1
SATL1	NM_001012980.2 link	c.1762C>T	p.Gln588*	stop_gained	Exon 3 of 5		NP_001012998.2	Q86VE3-2
SATL1	XM_047442081.1 link	c.1762C>T	p.Gln588*	stop_gained	Exon 4 of 7		XP_047298037.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SATL1	ENST00000644105.2 link	c.1762C>T	p.Gln588*	stop_gained	Exon 5 of 8		NM_001367857.2	ENSP00000494345.1		Q86VE3-1

Frequencies

GnomAD3 genomes

AF:

0.000116

AC:

AN:

112020

Hom.:

Cov.:

AF XY:

0.000234

AC XY:

AN XY:

34210

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00448

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000188

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.000617

AC:

104

AN:

168568

Hom.:

AF XY:

0.00116

AC XY:

AN XY:

56918

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00596

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.000296

AC:

315

AN:

1063874

Hom.:

Cov.:

AF XY:

0.000542

AC XY:

182

AN XY:

335940

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00575

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.000289

GnomAD4 genome

AF:

0.000116

AC:

AN:

112075

Hom.:

Cov.:

AF XY:

0.000233

AC XY:

AN XY:

34275

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00449

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000188

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.0000481

Hom.:

ExAC

AF:

0.000837

AC:

101

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

SATL1-related disorder

Benign:1

Jul 01, 2019

PreventionGenetics, part of Exact Sciences

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as likely 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

BayesDel_addAF

Uncertain

0.025

BayesDel_noAF

Pathogenic

0.27

CADD

Pathogenic

DANN

Benign

0.93

FATHMM_MKL

Benign

0.044

Vest4

0.053

GERP RS

-0.22

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.32

Details are displayed if max score is > 0.2

DS_DL_spliceai

0.32

Position offset: -12

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