Variant rs13043248 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_020436.5(SALL4):c.2037C>T(p.Thr679=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0915 in 1,613,982 control chromosomes in the GnomAD database, including 7,417 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.072 ( 539 hom., cov: 32)

Exomes 𝑓: 0.093 ( 6878 hom. )

Consequence

SALL4
NM_020436.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: -7.05

Variant links:

Genes affected

SALL4 (HGNC:15924): (spalt like transcription factor 4) This gene encodes a zinc finger transcription factor thought to play a role in the development of abducens motor neurons. Defects in this gene are a cause of Duane-radial ray syndrome (DRRS). Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015]

SALL4 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

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

BP6

Variant 20-51790446-G-A is Benign according to our data. Variant chr20-51790446-G-A is described in ClinVar as [Benign]. Clinvar id is 261261.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr20-51790446-G-A is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-7.05 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.104 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
SALL4	NM_020436.5 linkuse as main transcript	c.2037C>T	p.Thr679=	synonymous_variant	2/4	ENST00000217086.9
SALL4	XM_047440318.1 linkuse as main transcript	c.1731C>T	p.Thr577=	synonymous_variant	2/4
SALL4	NM_001318031.2 linkuse as main transcript	c.1150+887C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SALL4	ENST00000217086.9 linkuse as main transcript	c.2037C>T	p.Thr679=	synonymous_variant	2/4	1	NM_020436.5	P1	Q9UJQ4-1
SALL4	ENST00000371539.7 linkuse as main transcript	c.131-1305C>T		intron_variant		1
SALL4	ENST00000395997.3 linkuse as main transcript	c.1150+887C>T		intron_variant		1			Q9UJQ4-2

Frequencies

GnomAD3 genomes

AF:

0.0725

AC:

11024

AN:

152060

Hom.:

540

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0210

Gnomad AMI

AF:

0.123

Gnomad AMR

AF:

0.0699

Gnomad ASJ

AF:

0.0807

Gnomad EAS

AF:

0.0319

Gnomad SAS

AF:

0.0460

Gnomad FIN

AF:

0.0838

Gnomad MID

AF:

0.0791

Gnomad NFE

AF:

0.106

Gnomad OTH

AF:

0.0895

GnomAD3 exomes

AF:

0.0755

AC:

18971

AN:

251148

Hom.:

875

AF XY:

0.0769

AC XY:

10445

AN XY:

135758

show subpopulations

Gnomad AFR exome

AF:

0.0182

Gnomad AMR exome

AF:

0.0480

Gnomad ASJ exome

AF:

0.0888

Gnomad EAS exome

AF:

0.0274

Gnomad SAS exome

AF:

0.0445

Gnomad FIN exome

AF:

0.0901

Gnomad NFE exome

AF:

0.104

Gnomad OTH exome

AF:

0.0865

GnomAD4 exome

AF:

0.0935

AC:

136607

AN:

1461804

Hom.:

6878

Cov.:

AF XY:

0.0924

AC XY:

67173

AN XY:

727206

show subpopulations

Gnomad4 AFR exome

AF:

0.0185

Gnomad4 AMR exome

AF:

0.0490

Gnomad4 ASJ exome

AF:

0.0876

Gnomad4 EAS exome

AF:

0.0411

Gnomad4 SAS exome

AF:

0.0456

Gnomad4 FIN exome

AF:

0.0912

Gnomad4 NFE exome

AF:

0.103

Gnomad4 OTH exome

AF:

0.0906

GnomAD4 genome

AF:

0.0724

AC:

11015

AN:

152178

Hom.:

539

Cov.:

AF XY:

0.0703

AC XY:

5229

AN XY:

74402

show subpopulations

Gnomad4 AFR

AF:

0.0209

Gnomad4 AMR

AF:

0.0698

Gnomad4 ASJ

AF:

0.0807

Gnomad4 EAS

AF:

0.0320

Gnomad4 SAS

AF:

0.0460

Gnomad4 FIN

AF:

0.0838

Gnomad4 NFE

AF:

0.106

Gnomad4 OTH

AF:

0.0871

Alfa

AF:

0.0980

Hom.:

1033

Bravo

AF:

0.0685

Asia WGS

AF:

0.0370

AC:

130

AN:

3478

EpiCase

AF:

0.104

EpiControl

AF:

0.102

ClinVar

Significance: Benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:4

Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Benign, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Benign, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -

Duane-radial ray syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 30, 2024

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 03, 2015

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.0070

DANN

Benign

0.49

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