Variant X-85107504-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2

The NM_001367857.2(SATL1):c.1465C>T(p.Pro489Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000911 in 1,098,188 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 5 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in Lovd as Likely benign (no stars).

Frequency

Genomes: not found (cov: 24)

Exomes 𝑓: 0.0000091 ( 0 hom. 5 hem. )

Consequence

SATL1
NM_001367857.2 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -2.00

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.

BP4

Computational evidence support a benign effect (MetaRNN=0.061559588).

BP6

Variant X-85107504-G-A is Benign according to our data. Variant chrX-85107504-G-A is described in Lovd as [Likely_benign].

BS2

High Hemizygotes in GnomAdExome4 at 5 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SATL1	NM_001367857.2 linkuse as main transcript	c.1465C>T	p.Pro489Ser	missense_variant	3/8	ENST00000644105.2	NP_001354786.1
SATL1	NM_001367858.2 linkuse as main transcript	c.1465C>T	p.Pro489Ser	missense_variant	7/12		NP_001354787.1
SATL1	NM_001012980.2 linkuse as main transcript	c.1465C>T	p.Pro489Ser	missense_variant	1/5		NP_001012998.2	Q86VE3-2
SATL1	XM_047442081.1 linkuse as main transcript	c.1465C>T	p.Pro489Ser	missense_variant	2/7		XP_047298037.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SATL1	ENST00000644105.2 linkuse as main transcript	c.1465C>T	p.Pro489Ser	missense_variant	3/8		NM_001367857.2	ENSP00000494345.1		Q86VE3-1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.0000109

AC:

AN:

183370

Hom.:

AF XY:

0.0000295

AC XY:

AN XY:

67834

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

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:

0.0000244

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000911

AC:

AN:

1098188

Hom.:

Cov.:

AF XY:

0.0000138

AC XY:

AN XY:

363552

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

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:

0.0000107

Gnomad4 OTH exome

AF:

0.0000217

GnomAD4 genome

Cov.:

ExAC

AF:

0.0000165

AC:

EpiCase

AF:

0.00

EpiControl

AF:

0.000119

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Oct 04, 2024

The c.1465C>T (p.P489S) alteration is located in exon 1 (coding exon 1) of the SATL1 gene. This alteration results from a C to T substitution at nucleotide position 1465, causing the proline (P) at amino acid position 489 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.084

BayesDel_addAF

Benign

-0.46

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.58

DANN

Uncertain

0.99

DEOGEN2

Benign

0.017

T;.;.;.;.

FATHMM_MKL

Benign

0.013

LIST_S2

Benign

0.52

.;T;T;.;T

M_CAP

Benign

0.067

MetaRNN

Benign

0.062

T;T;T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.2

L;.;.;.;.

PrimateAI

Benign

0.18

PROVEAN

Benign

-1.1

N;N;.;.;.

REVEL

Benign

0.017

Sift

Benign

0.41

T;T;.;.;.

Sift4G

Benign

0.20

T;T;.;.;.

Polyphen

0.68

P;.;.;.;.

Vest4

0.030

MutPred

0.22

Gain of phosphorylation at P302 (P = 0.0493);.;.;.;.;

MVP

0.22

MPC

0.35

ClinPred

0.057

GERP RS

0.29

Varity_R

0.031

gMVP

0.18

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