Variant X-85107644-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BS1BS2

The NM_001367857.2(SATL1):c.1325G>A(p.Trp442Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00145 in 1,210,757 control chromosomes in the GnomAD database, including 12 homozygotes. There are 504 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: 𝑓 0.0071 ( 8 hom., 225 hem., cov: 24)

Exomes 𝑓: 0.00087 ( 4 hom. 279 hem. )

Consequence

SATL1
NM_001367857.2 stop_gained

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.457

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.

BP6

Variant X-85107644-C-T is Benign according to our data. Variant chrX-85107644-C-T is described in ClinVar as [Benign]. Clinvar id is 3044194.Status of the report is no_assertion_criteria_provided, 0 stars.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00708 (797/112632) while in subpopulation AFR AF= 0.023 (714/30982). AF 95% confidence interval is 0.0216. There are 8 homozygotes in gnomad4. There are 225 alleles in male gnomad4 subpopulation. Median coverage is 24. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 8 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
SATL1	NM_001367857.2 linkuse as main transcript	c.1325G>A	p.Trp442Ter	stop_gained	3/8	ENST00000644105.2
SATL1	NM_001367858.2 linkuse as main transcript	c.1325G>A	p.Trp442Ter	stop_gained	7/12
SATL1	NM_001012980.2 linkuse as main transcript	c.1325G>A	p.Trp442Ter	stop_gained	1/5
SATL1	XM_047442081.1 linkuse as main transcript	c.1325G>A	p.Trp442Ter	stop_gained	2/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SATL1	ENST00000644105.2 linkuse as main transcript	c.1325G>A	p.Trp442Ter	stop_gained	3/8		NM_001367857.2	A2	Q86VE3-1

Frequencies

GnomAD3 genomes

AF:

0.00706

AC:

795

AN:

112581

Hom.:

Cov.:

AF XY:

0.00646

AC XY:

225

AN XY:

34853

show subpopulations

Gnomad AFR

AF:

0.0230

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00552

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000338

Gnomad OTH

AF:

0.00396

GnomAD3 exomes

AF:

0.00209

AC:

383

AN:

183448

Hom.:

AF XY:

0.00147

AC XY:

100

AN XY:

67902

show subpopulations

Gnomad AFR exome

AF:

0.0220

Gnomad AMR exome

AF:

0.00277

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:

0.000134

Gnomad OTH exome

AF:

0.00155

GnomAD4 exome

AF:

0.000870

AC:

955

AN:

1098125

Hom.:

Cov.:

AF XY:

0.000767

AC XY:

279

AN XY:

363595

show subpopulations

Gnomad4 AFR exome

AF:

0.0232

Gnomad4 AMR exome

AF:

0.00293

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:

0.000137

Gnomad4 OTH exome

AF:

0.00252

GnomAD4 genome

AF:

0.00708

AC:

797

AN:

112632

Hom.:

Cov.:

AF XY:

0.00644

AC XY:

225

AN XY:

34914

show subpopulations

Gnomad4 AFR

AF:

0.0230

Gnomad4 AMR

AF:

0.00551

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000338

Gnomad4 OTH

AF:

0.00391

Alfa

AF:

0.000930

Hom.:

Bravo

AF:

0.00854

ESP6500AA

AF:

0.0196

AC:

ESP6500EA

AF:

0.000149

AC:

ExAC

AF:

0.00219

AC:

266

EpiCase

AF:

0.0000545

EpiControl

AF:

0.0000593

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

Nov 07, 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

BayesDel_addAF

Benign

-0.072

BayesDel_noAF

Pathogenic

0.14

CADD

Pathogenic

DANN

Benign

0.88

FATHMM_MKL

Benign

0.019

MutationTaster

Benign

1.0

A;A;A

Vest4

0.034

GERP RS

-0.81

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