NM_002968.3:c.469_477delAGCAGCAGC

Variant names:

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BS1BS2

The NM_002968.3(SALL1):c.469_477delAGCAGCAGC(p.Ser157_Ser159del) variant causes a conservative inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00356 in 1,580,006 control chromosomes in the GnomAD database, including 20 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.0023 ( 0 hom., cov: 31)

Exomes 𝑓: 0.0037 ( 20 hom. )

Consequence

SALL1
NM_002968.3 conservative_inframe_deletion

Scores

Not classified

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1B:9

Conservation

PhyloP100: 1.79

Variant links:

Genes affected

SALL1 (HGNC:10524): (spalt like transcription factor 1) The protein encoded by this gene is a zinc finger transcriptional repressor and may be part of the NuRD histone deacetylase complex (HDAC). Defects in this gene are a cause of Townes-Brocks syndrome (TBS) as well as bronchio-oto-renal syndrome (BOR). Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

SALL1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP6

Variant 16-51141744-CGCTGCTGCT-C is Benign according to our data. Variant chr16-51141744-CGCTGCTGCT-C is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 224343.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=3, Benign=2, Uncertain_significance=1}. Variant chr16-51141744-CGCTGCTGCT-C is described in Lovd as [Likely_benign]. Variant chr16-51141744-CGCTGCTGCT-C is described in Lovd as [Likely_benign]. Variant chr16-51141744-CGCTGCTGCT-C is described in Lovd as [Benign].

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00234 (354/151106) while in subpopulation NFE AF= 0.00386 (261/67694). AF 95% confidence interval is 0.00347. There are 0 homozygotes in gnomad4. There are 170 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.

BS2

High AC in GnomAd4 at 354 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SALL1	NM_002968.3 link	c.469_477delAGCAGCAGC	p.Ser157_Ser159del	conservative_inframe_deletion	Exon 2 of 3	ENST00000251020.9	NP_002959.2	Q9NSC2-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SALL1	ENST00000251020.9 link	c.469_477delAGCAGCAGC	p.Ser157_Ser159del	conservative_inframe_deletion	Exon 2 of 3	1	NM_002968.3	ENSP00000251020.4		Q9NSC2-1

Frequencies

GnomAD3 genomes

AF:

0.00234

AC:

354

AN:

150996

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000877

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00237

Gnomad ASJ

AF:

0.000290

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000211

Gnomad FIN

AF:

0.00144

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00386

Gnomad OTH

AF:

0.00192

GnomAD3 exomes

AF:

0.00285

AC:

609

AN:

213596

Hom.:

AF XY:

0.00281

AC XY:

324

AN XY:

115304

show subpopulations

Gnomad AFR exome

AF:

0.00103

Gnomad AMR exome

AF:

0.00286

Gnomad ASJ exome

AF:

0.00274

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000389

Gnomad FIN exome

AF:

0.00124

Gnomad NFE exome

AF:

0.00452

Gnomad OTH exome

AF:

0.00470

GnomAD4 exome

AF:

0.00369

AC:

5270

AN:

1428900

Hom.:

AF XY:

0.00361

AC XY:

2564

AN XY:

710684

show subpopulations

Gnomad4 AFR exome

AF:

0.000825

Gnomad4 AMR exome

AF:

0.00216

Gnomad4 ASJ exome

AF:

0.00259

Gnomad4 EAS exome

AF:

0.0000779

Gnomad4 SAS exome

AF:

0.0000476

Gnomad4 FIN exome

AF:

0.00160

Gnomad4 NFE exome

AF:

0.00443

Gnomad4 OTH exome

AF:

0.00291

GnomAD4 genome

AF:

0.00234

AC:

354

AN:

151106

Hom.:

Cov.:

AF XY:

0.00230

AC XY:

170

AN XY:

73818

show subpopulations

Gnomad4 AFR

AF:

0.000875

Gnomad4 AMR

AF:

0.00237

Gnomad4 ASJ

AF:

0.000290

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000211

Gnomad4 FIN

AF:

0.00144

Gnomad4 NFE

AF:

0.00386

Gnomad4 OTH

AF:

0.00190

Bravo

AF:

0.00230

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:1Benign:9

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

not provided

Benign:6

Apr 17, 2021

GeneDx

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 27657687) -

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Feb 01, 2025

CeGaT Center for Human Genetics Tuebingen

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

SALL1: BS1, BS2 -

Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Genome Diagnostics Laboratory, University Medical Center Utrecht

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

not specified

Benign:2

Aug 30, 2016

Eurofins Ntd Llc (ga)

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jul 09, 2020

Genetic Services Laboratory, University of Chicago

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Townes-Brocks syndrome 1

Uncertain:1

Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: research

- -

Townes syndrome

Benign:1

Dec 24, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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