Variant rs17802735 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.2640G>C(p.Ser880=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 1,614,150 control chromosomes in the GnomAD database, including 12,275 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.088 ( 811 hom., cov: 32)

Exomes 𝑓: 0.12 ( 11464 hom. )

Consequence

SALL4
NM_020436.5 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -5.38

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=-0.78).

BP6

Variant 20-51788963-C-G is Benign according to our data. Variant chr20-51788963-C-G is described in ClinVar as [Benign]. Clinvar id is 261263.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr20-51788963-C-G is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-5.38 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
SALL4	NM_020436.5 linkuse as main transcript	c.2640G>C	p.Ser880=	synonymous_variant	3/4	ENST00000217086.9	NP_065169.1
SALL4	NM_001318031.2 linkuse as main transcript	c.1329G>C	p.Ser443=	synonymous_variant	3/4		NP_001304960.1
SALL4	XM_047440318.1 linkuse as main transcript	c.2334G>C	p.Ser778=	synonymous_variant	3/4		XP_047296274.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SALL4	ENST00000217086.9 linkuse as main transcript	c.2640G>C	p.Ser880=	synonymous_variant	3/4	1	NM_020436.5	ENSP00000217086	P1	Q9UJQ4-1
SALL4	ENST00000395997.3 linkuse as main transcript	c.1329G>C	p.Ser443=	synonymous_variant	3/4	1		ENSP00000379319		Q9UJQ4-2
SALL4	ENST00000371539.7 linkuse as main transcript	c.309G>C	p.Ser103=	synonymous_variant	2/3	1		ENSP00000360594

Frequencies

GnomAD3 genomes

AF:

0.0877

AC:

13341

AN:

152168

Hom.:

811

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0227

Gnomad AMI

AF:

0.153

Gnomad AMR

AF:

0.0809

Gnomad ASJ

AF:

0.0698

Gnomad EAS

AF:

0.00135

Gnomad SAS

AF:

0.0697

Gnomad FIN

AF:

0.108

Gnomad MID

AF:

0.0918

Gnomad NFE

AF:

0.134

Gnomad OTH

AF:

0.0740

GnomAD3 exomes

AF:

0.0916

AC:

23021

AN:

251444

Hom.:

1317

AF XY:

0.0945

AC XY:

12842

AN XY:

135906

show subpopulations

Gnomad AFR exome

AF:

0.0223

Gnomad AMR exome

AF:

0.0481

Gnomad ASJ exome

AF:

0.0750

Gnomad EAS exome

AF:

0.000598

Gnomad SAS exome

AF:

0.0772

Gnomad FIN exome

AF:

0.108

Gnomad NFE exome

AF:

0.131

Gnomad OTH exome

AF:

0.0945

GnomAD4 exome

AF:

0.120

AC:

175852

AN:

1461864

Hom.:

11464

Cov.:

AF XY:

0.119

AC XY:

86581

AN XY:

727234

show subpopulations

Gnomad4 AFR exome

AF:

0.0184

Gnomad4 AMR exome

AF:

0.0515

Gnomad4 ASJ exome

AF:

0.0734

Gnomad4 EAS exome

AF:

0.000353

Gnomad4 SAS exome

AF:

0.0770

Gnomad4 FIN exome

AF:

0.108

Gnomad4 NFE exome

AF:

0.137

Gnomad4 OTH exome

AF:

0.104

GnomAD4 genome

AF:

0.0876

AC:

13339

AN:

152286

Hom.:

811

Cov.:

AF XY:

0.0863

AC XY:

6426

AN XY:

74466

show subpopulations

Gnomad4 AFR

AF:

0.0226

Gnomad4 AMR

AF:

0.0808

Gnomad4 ASJ

AF:

0.0698

Gnomad4 EAS

AF:

0.00135

Gnomad4 SAS

AF:

0.0698

Gnomad4 FIN

AF:

0.108

Gnomad4 NFE

AF:

0.134

Gnomad4 OTH

AF:

0.0733

Alfa

AF:

0.0916

Hom.:

294

Bravo

AF:

0.0812

EpiCase

AF:

0.129

EpiControl

AF:

0.126

ClinVar

Significance: Benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

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	PreventionGenetics, part of Exact Sciences	-	- -
Benign, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 03, 2015	- -

Duane-radial ray syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 31, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

0.011

DANN

Benign

0.55

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