rs3746609

Positions:

chr20-32434666-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_015338.6(ASXL1):c.1954G>A(p.Gly652Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00672 in 1,602,238 control chromosomes in the GnomAD database, including 401 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0087 ( 35 hom., cov: 32)

Exomes 𝑓: 0.0065 ( 366 hom. )

Consequence

ASXL1
NM_015338.6 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:7O:1

Conservation

PhyloP100: 0.730

Variant links:

Genes affected

ASXL1 (HGNC:18318): (ASXL transcriptional regulator 1) This gene is similar to the Drosophila additional sex combs gene, which encodes a chromatin-binding protein required for normal determination of segment identity in the developing embryo. The protein is a member of the Polycomb group of proteins, which are necessary for the maintenance of stable repression of homeotic and other loci. The protein is thought to disrupt chromatin in localized areas, enhancing transcription of certain genes while repressing the transcription of other genes. The protein encoded by this gene functions as a ligand-dependent co-activator for retinoic acid receptor in cooperation with nuclear receptor coactivator 1. Mutations in this gene are associated with myelodysplastic syndromes and chronic myelomonocytic leukemia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2009]

ASXL1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.001430273).

BP6

Variant 20-32434666-G-A is Benign according to our data. Variant chr20-32434666-G-A is described in ClinVar as [Benign]. Clinvar id is 133592.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr20-32434666-G-A is described in Lovd as [Benign]. Variant chr20-32434666-G-A is described in Lovd as [Likely_benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0656 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ASXL1	NM_015338.6 linkuse as main transcript	c.1954G>A	p.Gly652Ser	missense_variant	13/13	ENST00000375687.10	NP_056153.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ASXL1	ENST00000375687.10 linkuse as main transcript	c.1954G>A	p.Gly652Ser	missense_variant	13/13	5	NM_015338.6	ENSP00000364839	P1	Q8IXJ9-1

Frequencies

GnomAD3 genomes

AF:

0.00870

AC:

1323

AN:

152112

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00200

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0360

Gnomad ASJ

AF:

0.00980

Gnomad EAS

AF:

0.0719

Gnomad SAS

AF:

0.00580

Gnomad FIN

AF:

0.0112

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00165

Gnomad OTH

AF:

0.0119

GnomAD3 exomes

AF:

0.0191

AC:

4317

AN:

225642

Hom.:

173

AF XY:

0.0155

AC XY:

1931

AN XY:

124220

show subpopulations

Gnomad AFR exome

AF:

0.00126

Gnomad AMR exome

AF:

0.0803

Gnomad ASJ exome

AF:

0.00741

Gnomad EAS exome

AF:

0.0624

Gnomad SAS exome

AF:

0.00248

Gnomad FIN exome

AF:

0.00959

Gnomad NFE exome

AF:

0.00235

Gnomad OTH exome

AF:

0.0176

GnomAD4 exome

AF:

0.00651

AC:

9435

AN:

1450008

Hom.:

366

Cov.:

AF XY:

0.00608

AC XY:

4382

AN XY:

720604

show subpopulations

Gnomad4 AFR exome

AF:

0.00112

Gnomad4 AMR exome

AF:

0.0734

Gnomad4 ASJ exome

AF:

0.00762

Gnomad4 EAS exome

AF:

0.0938

Gnomad4 SAS exome

AF:

0.00291

Gnomad4 FIN exome

AF:

0.0102

Gnomad4 NFE exome

AF:

0.000967

Gnomad4 OTH exome

AF:

0.00837

GnomAD4 genome

AF:

0.00874

AC:

1330

AN:

152230

Hom.:

Cov.:

AF XY:

0.00956

AC XY:

712

AN XY:

74440

show subpopulations

Gnomad4 AFR

AF:

0.00200

Gnomad4 AMR

AF:

0.0367

Gnomad4 ASJ

AF:

0.00980

Gnomad4 EAS

AF:

0.0716

Gnomad4 SAS

AF:

0.00560

Gnomad4 FIN

AF:

0.0112

Gnomad4 NFE

AF:

0.00165

Gnomad4 OTH

AF:

0.0113

Alfa

AF:

0.00418

Hom.:

Bravo

AF:

0.0118

ESP6500AA

AF:

0.00195

AC:

ESP6500EA

AF:

0.00208

AC:

ExAC

AF:

0.0154

AC:

1854

Asia WGS

AF:

0.0520

AC:

180

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:7Other:1

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:4

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 31, 2018	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -
Likely benign, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:2Other:1

not provided, no classification provided	reference population	ITMI	Sep 19, 2013	- -
Benign, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Oct 06, 2015	- -

Bohring-Opitz syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Dec 05, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.069

BayesDel_addAF

Benign

-0.63

BayesDel_noAF

Benign

-0.57

CADD

Benign

DANN

Benign

0.90

DEOGEN2

Benign

0.052

T;T;T;.;T

Eigen

Benign

-0.72

Eigen_PC

Benign

-0.56

FATHMM_MKL

Uncertain

0.87

LIST_S2

Benign

0.72

.;T;.;T;T

MetaRNN

Benign

0.0014

T;T;T;T;T

MetaSVM

Benign

-0.99

MutationAssessor

Benign

0.74

N;N;N;.;.

MutationTaster

Benign

1.0

N;N

PrimateAI

Benign

0.35

PROVEAN

Benign

-0.51

N;.;.;.;N

REVEL

Benign

0.017

Sift

Benign

0.65

T;.;.;.;T

Sift4G

Benign

0.49

T;T;T;.;T

Polyphen

0.0040

B;B;B;.;.

Vest4

0.20

MPC

0.059

ClinPred

0.0027

GERP RS

2.0

RBP_binding_hub_radar

1.1

RBP_regulation_power_radar

4.0

Varity_R

0.042

gMVP

0.10

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