Variant chrX-85094935-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BS1BS2

The NM_001367857.2(SATL1):c.1755C>T(p.Asn585=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0218 in 1,178,147 control chromosomes in the GnomAD database, including 254 homozygotes. There are 8,287 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.017 ( 19 hom., 549 hem., cov: 23)

Exomes 𝑓: 0.022 ( 235 hom. 7738 hem. )

Consequence

SATL1
NM_001367857.2 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -2.19

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 -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant X-85094935-G-A is Benign according to our data. Variant chrX-85094935-G-A is described in ClinVar as [Benign]. Clinvar id is 3037120.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-2.19 with no splicing effect.

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0168 (1878/111768) while in subpopulation SAS AF= 0.0391 (104/2658). AF 95% confidence interval is 0.033. There are 19 homozygotes in gnomad4. There are 549 alleles in male gnomad4 subpopulation. Median coverage is 23. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 19 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
SATL1	NM_001367857.2 linkuse as main transcript	c.1755C>T	p.Asn585=	synonymous_variant	5/8	ENST00000644105.2
SATL1	NM_001367858.2 linkuse as main transcript	c.1755C>T	p.Asn585=	synonymous_variant	9/12
SATL1	NM_001012980.2 linkuse as main transcript	c.1755C>T	p.Asn585=	synonymous_variant	3/5
SATL1	XM_047442081.1 linkuse as main transcript	c.1755C>T	p.Asn585=	synonymous_variant	4/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SATL1	ENST00000644105.2 linkuse as main transcript	c.1755C>T	p.Asn585=	synonymous_variant	5/8		NM_001367857.2	A2	Q86VE3-1

Frequencies

GnomAD3 genomes

AF:

0.0168

AC:

1880

AN:

111715

Hom.:

Cov.:

AF XY:

0.0162

AC XY:

548

AN XY:

33919

show subpopulations

Gnomad AFR

AF:

0.00296

Gnomad AMI

AF:

0.0959

Gnomad AMR

AF:

0.00949

Gnomad ASJ

AF:

0.0510

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0394

Gnomad FIN

AF:

0.0147

Gnomad MID

AF:

0.0378

Gnomad NFE

AF:

0.0237

Gnomad OTH

AF:

0.0166

GnomAD3 exomes

AF:

0.0206

AC:

3500

AN:

169951

Hom.:

AF XY:

0.0233

AC XY:

1350

AN XY:

57857

show subpopulations

Gnomad AFR exome

AF:

0.00216

Gnomad AMR exome

AF:

0.00687

Gnomad ASJ exome

AF:

0.0544

Gnomad EAS exome

AF:

0.000148

Gnomad SAS exome

AF:

0.0478

Gnomad FIN exome

AF:

0.0155

Gnomad NFE exome

AF:

0.0235

Gnomad OTH exome

AF:

0.0230

GnomAD4 exome

AF:

0.0223

AC:

23763

AN:

1066379

Hom.:

235

Cov.:

AF XY:

0.0229

AC XY:

7738

AN XY:

337845

show subpopulations

Gnomad4 AFR exome

AF:

0.00220

Gnomad4 AMR exome

AF:

0.00770

Gnomad4 ASJ exome

AF:

0.0521

Gnomad4 EAS exome

AF:

0.000166

Gnomad4 SAS exome

AF:

0.0480

Gnomad4 FIN exome

AF:

0.0149

Gnomad4 NFE exome

AF:

0.0223

Gnomad4 OTH exome

AF:

0.0227

GnomAD4 genome

AF:

0.0168

AC:

1878

AN:

111768

Hom.:

Cov.:

AF XY:

0.0162

AC XY:

549

AN XY:

33982

show subpopulations

Gnomad4 AFR

AF:

0.00295

Gnomad4 AMR

AF:

0.00948

Gnomad4 ASJ

AF:

0.0510

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0391

Gnomad4 FIN

AF:

0.0147

Gnomad4 NFE

AF:

0.0237

Gnomad4 OTH

AF:

0.0164

Alfa

AF:

0.0256

Hom.:

249

Bravo

AF:

0.0153

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

Jan 20, 2020

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_noAF

Benign

-0.90

CADD

Benign

0.21

DANN

Benign

0.36

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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