Genetic Variant SATL1:p.Arg476Arg (chrX-85107541-C-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS2

The NM_001367857.2(SATL1):c.1428G>A(p.Arg476Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000783 in 1,210,808 control chromosomes in the GnomAD database, including 7 homozygotes. There are 239 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 0.0044 ( 3 hom., 137 hem., cov: 24)

Exomes 𝑓: 0.00041 ( 4 hom. 102 hem. )

Consequence

SATL1
NM_001367857.2 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -6.59

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 -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant X-85107541-C-T is Benign according to our data. Variant chrX-85107541-C-T is described in ClinVar as [Benign]. Clinvar id is 3044223.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-6.59 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 3 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SATL1	NM_001367857.2 link	c.1428G>A	p.Arg476Arg	synonymous_variant	Exon 3 of 8	ENST00000644105.2	NP_001354786.1
SATL1	NM_001367858.2 link	c.1428G>A	p.Arg476Arg	synonymous_variant	Exon 7 of 12		NP_001354787.1
SATL1	NM_001012980.2 link	c.1428G>A	p.Arg476Arg	synonymous_variant	Exon 1 of 5		NP_001012998.2	Q86VE3-2
SATL1	XM_047442081.1 link	c.1428G>A	p.Arg476Arg	synonymous_variant	Exon 2 of 7		XP_047298037.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SATL1	ENST00000644105.2 link	c.1428G>A	p.Arg476Arg	synonymous_variant	Exon 3 of 8		NM_001367857.2	ENSP00000494345.1		Q86VE3-1

Frequencies

GnomAD3 genomes

AF:

0.00442

AC:

497

AN:

112551

Hom.:

Cov.:

AF XY:

0.00394

AC XY:

137

AN XY:

34733

show subpopulations

Gnomad AFR

AF:

0.0154

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00159

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00422

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00198

GnomAD3 exomes

AF:

0.00121

AC:

221

AN:

183310

Hom.:

AF XY:

0.000752

AC XY:

AN XY:

67794

show subpopulations

Gnomad AFR exome

AF:

0.0162

Gnomad AMR exome

AF:

0.000219

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:

0.0000122

Gnomad OTH exome

AF:

0.000221

GnomAD4 exome

AF:

0.000411

AC:

451

AN:

1098209

Hom.:

Cov.:

AF XY:

0.000281

AC XY:

102

AN XY:

363567

show subpopulations

Gnomad4 AFR exome

AF:

0.0150

Gnomad4 AMR exome

AF:

0.000426

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:

0.00000237

Gnomad4 OTH exome

AF:

0.000781

GnomAD4 genome

AF:

0.00441

AC:

497

AN:

112599

Hom.:

Cov.:

AF XY:

0.00394

AC XY:

137

AN XY:

34791

show subpopulations

Gnomad4 AFR

AF:

0.0153

Gnomad4 AMR

AF:

0.00159

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.00195

Alfa

AF:

0.00123

Hom.:

Bravo

AF:

0.00531

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

Jun 07, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

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

-0.85

CADD

Benign

0.64

DANN

Benign

0.38

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