Variant X-85095004-A-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001367857.2(SATL1):c.1694-8T>C variant causes a splice region, splice polypyrimidine tract, 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 0.64 ( 15838 hom., 21055 hem., cov: 22)

Exomes 𝑓: 0.69 ( 152733 hom. 188388 hem. )

Failed GnomAD Quality Control

Consequence

SATL1
NM_001367857.2 splice_region, splice_polypyrimidine_tract, intron

Scores

Splicing: ADA: 0.0004465

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.393

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=-0.77).

BP6

Variant X-85095004-A-G is Benign according to our data. Variant chrX-85095004-A-G is described in ClinVar as [Benign]. Clinvar id is 3059185.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
SATL1	NM_001367857.2 linkuse as main transcript	c.1694-8T>C	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant	ENST00000644105.2
SATL1	NM_001012980.2 linkuse as main transcript	c.1694-8T>C	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant
SATL1	NM_001367858.2 linkuse as main transcript	c.1694-8T>C	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant
SATL1	XM_047442081.1 linkuse as main transcript	c.1694-8T>C	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SATL1	ENST00000644105.2 linkuse as main transcript	c.1694-8T>C		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant			NM_001367857.2	A2	Q86VE3-1

Frequencies

GnomAD3 genomes

AF:

0.636

AC:

70235

AN:

110415

Hom.:

15847

Cov.:

AF XY:

0.643

AC XY:

21030

AN XY:

32685

show subpopulations

Gnomad AFR

AF:

0.508

Gnomad AMI

AF:

0.588

Gnomad AMR

AF:

0.685

Gnomad ASJ

AF:

0.738

Gnomad EAS

AF:

0.642

Gnomad SAS

AF:

0.811

Gnomad FIN

AF:

0.729

Gnomad MID

AF:

0.787

Gnomad NFE

AF:

0.675

Gnomad OTH

AF:

0.662

GnomAD3 exomes

AF:

0.682

AC:

108374

AN:

158818

Hom.:

24646

AF XY:

0.701

AC XY:

35722

AN XY:

50938

show subpopulations

Gnomad AFR exome

AF:

0.503

Gnomad AMR exome

AF:

0.664

Gnomad ASJ exome

AF:

0.727

Gnomad EAS exome

AF:

0.637

Gnomad SAS exome

AF:

0.810

Gnomad FIN exome

AF:

0.736

Gnomad NFE exome

AF:

0.680

Gnomad OTH exome

AF:

0.697

GnomAD4 exome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.685

AC:

638444

AN:

931580

Hom.:

152733

Cov.:

AF XY:

0.711

AC XY:

188388

AN XY:

264848

show subpopulations

Gnomad4 AFR exome

AF:

0.509

Gnomad4 AMR exome

AF:

0.673

Gnomad4 ASJ exome

AF:

0.731

Gnomad4 EAS exome

AF:

0.676

Gnomad4 SAS exome

AF:

0.815

Gnomad4 FIN exome

AF:

0.727

Gnomad4 NFE exome

AF:

0.680

Gnomad4 OTH exome

AF:

0.674

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.636

AC:

70248

AN:

110468

Hom.:

15838

Cov.:

AF XY:

0.643

AC XY:

21055

AN XY:

32748

show subpopulations

Gnomad4 AFR

AF:

0.507

Gnomad4 AMR

AF:

0.685

Gnomad4 ASJ

AF:

0.738

Gnomad4 EAS

AF:

0.643

Gnomad4 SAS

AF:

0.813

Gnomad4 FIN

AF:

0.729

Gnomad4 NFE

AF:

0.675

Gnomad4 OTH

AF:

0.659

Alfa

AF:

0.664

Hom.:

8524

Bravo

AF:

0.625

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

Oct 16, 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_noAF

Benign

-0.77

CADD

Benign

7.9

DANN

Benign

0.71

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00045

dbscSNV1_RF

Benign

0.020

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