Genetic Variant SATL1:c.1693+6G>A (chrX-85103858-C-T) – ACMG Classification: Likely_benign (-5 pts)

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP6

The NM_001367857.2(SATL1):c.1693+6G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.74 ( 21638 hom., 24349 hem., cov: 23)

Exomes 𝑓: 0.69 ( 174727 hom. 233632 hem. )

Failed GnomAD Quality Control

Consequence

SATL1
NM_001367857.2 splice_region, intron

Scores

Splicing: ADA: 0.00005763

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.0690

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.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BP6

Variant X-85103858-C-T is Benign according to our data. Variant chrX-85103858-C-T is described in ClinVar as [Benign]. Clinvar id is 3059876.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
SATL1	NM_001367857.2 link	c.1693+6G>A	splice_region_variant, intron_variant	Intron 4 of 7	ENST00000644105.2	NP_001354786.1
SATL1	NM_001367858.2 link	c.1693+6G>A	splice_region_variant, intron_variant	Intron 8 of 11		NP_001354787.1
SATL1	NM_001012980.2 link	c.1693+6G>A	splice_region_variant, intron_variant	Intron 2 of 4		NP_001012998.2	Q86VE3-2
SATL1	XM_047442081.1 link	c.1693+6G>A	splice_region_variant, intron_variant	Intron 3 of 6		XP_047298037.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SATL1	ENST00000644105.2 link	c.1693+6G>A		splice_region_variant, intron_variant	Intron 4 of 7		NM_001367857.2	ENSP00000494345.1		Q86VE3-1

Frequencies

GnomAD3 genomes

AF:

0.743

AC:

81916

AN:

110228

Hom.:

21637

Cov.:

AF XY:

0.747

AC XY:

24282

AN XY:

32492

show subpopulations

Gnomad AFR

AF:

0.866

Gnomad AMI

AF:

0.584

Gnomad AMR

AF:

0.735

Gnomad ASJ

AF:

0.752

Gnomad EAS

AF:

0.682

Gnomad SAS

AF:

0.828

Gnomad FIN

AF:

0.734

Gnomad MID

AF:

0.819

Gnomad NFE

AF:

0.676

Gnomad OTH

AF:

0.761

GnomAD3 exomes

AF:

0.714

AC:

129332

AN:

181087

Hom.:

29474

AF XY:

0.717

AC XY:

47281

AN XY:

65947

show subpopulations

Gnomad AFR exome

AF:

0.867

Gnomad AMR exome

AF:

0.681

Gnomad ASJ exome

AF:

0.739

Gnomad EAS exome

AF:

0.674

Gnomad SAS exome

AF:

0.828

Gnomad FIN exome

AF:

0.732

Gnomad NFE exome

AF:

0.675

Gnomad OTH exome

AF:

0.714

GnomAD4 exome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.692

AC:

735235

AN:

1062699

Hom.:

174727

Cov.:

AF XY:

0.692

AC XY:

233632

AN XY:

337625

show subpopulations

Gnomad4 AFR exome

AF:

0.875

Gnomad4 AMR exome

AF:

0.693

Gnomad4 ASJ exome

AF:

0.739

Gnomad4 EAS exome

AF:

0.705

Gnomad4 SAS exome

AF:

0.832

Gnomad4 FIN exome

AF:

0.725

Gnomad4 NFE exome

AF:

0.673

Gnomad4 OTH exome

AF:

0.701

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.743

AC:

81979

AN:

110284

Hom.:

21638

Cov.:

AF XY:

0.748

AC XY:

24349

AN XY:

32558

show subpopulations

Gnomad4 AFR

AF:

0.866

Gnomad4 AMR

AF:

0.735

Gnomad4 ASJ

AF:

0.752

Gnomad4 EAS

AF:

0.682

Gnomad4 SAS

AF:

0.829

Gnomad4 FIN

AF:

0.734

Gnomad4 NFE

AF:

0.676

Gnomad4 OTH

AF:

0.759

Alfa

AF:

0.707

Hom.:

15629

Bravo

AF:

0.746

EpiCase

AF:

0.674

EpiControl

AF:

0.692

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

SATL1-related disorder

Benign:1

Oct 16, 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

-0.93

CADD

Benign

1.0

DANN

Benign

0.30

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000058

dbscSNV1_RF

Benign

0.0

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