Variant 16-51141744-CGCTGCTGCTGCTGCTGCT-CGCTGCTGCTGCTGCTGCTGCT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_002968.3(SALL1):c.475_477dupAGC(p.Ser159dup) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0219 in 1,579,498 control chromosomes in the GnomAD database, including 444 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.042 ( 289 hom., cov: 31)

Exomes 𝑓: 0.020 ( 155 hom. )

Consequence

SALL1
NM_002968.3 conservative_inframe_insertion

Scores

Not classified

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:9

Conservation

PhyloP100: 1.34

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 -16 ACMG points.

BP6

Variant 16-51141744-C-CGCT is Benign according to our data. Variant chr16-51141744-C-CGCT is described in ClinVar as [Likely_benign]. Clinvar id is 258874.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SALL1	NM_002968.3 linkuse as main transcript	c.475_477dupAGC	p.Ser159dup	conservative_inframe_insertion	2/3	ENST00000251020.9	NP_002959.2	Q9NSC2-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SALL1	ENST00000251020.9 linkuse as main transcript	c.475_477dupAGC	p.Ser159dup	conservative_inframe_insertion	2/3	1	NM_002968.3	ENSP00000251020.4		Q9NSC2-1

Frequencies

GnomAD3 genomes

AF:

0.0420

AC:

6342

AN:

150958

Hom.:

284

Cov.:

show subpopulations

Gnomad AFR

AF:

0.109

Gnomad AMI

AF:

0.00330

Gnomad AMR

AF:

0.0198

Gnomad ASJ

AF:

0.0302

Gnomad EAS

AF:

0.0189

Gnomad SAS

AF:

0.0192

Gnomad FIN

AF:

0.00354

Gnomad MID

AF:

0.0609

Gnomad NFE

AF:

0.0171

Gnomad OTH

AF:

0.0375

GnomAD3 exomes

AF:

0.0240

AC:

5119

AN:

213596

Hom.:

AF XY:

0.0219

AC XY:

2530

AN XY:

115304

show subpopulations

Gnomad AFR exome

AF:

0.109

Gnomad AMR exome

AF:

0.0182

Gnomad ASJ exome

AF:

0.0305

Gnomad EAS exome

AF:

0.0220

Gnomad SAS exome

AF:

0.0193

Gnomad FIN exome

AF:

0.00468

Gnomad NFE exome

AF:

0.0186

Gnomad OTH exome

AF:

0.0207

GnomAD4 exome

AF:

0.0198

AC:

28257

AN:

1428430

Hom.:

155

Cov.:

AF XY:

0.0192

AC XY:

13635

AN XY:

710460

show subpopulations

Gnomad4 AFR exome

AF:

0.108

Gnomad4 AMR exome

AF:

0.0169

Gnomad4 ASJ exome

AF:

0.0297

Gnomad4 EAS exome

AF:

0.0207

Gnomad4 SAS exome

AF:

0.0172

Gnomad4 FIN exome

AF:

0.00407

Gnomad4 NFE exome

AF:

0.0175

Gnomad4 OTH exome

AF:

0.0261

GnomAD4 genome

AF:

0.0422

AC:

6368

AN:

151068

Hom.:

289

Cov.:

AF XY:

0.0403

AC XY:

2972

AN XY:

73796

show subpopulations

Gnomad4 AFR

AF:

0.109

Gnomad4 AMR

AF:

0.0197

Gnomad4 ASJ

AF:

0.0302

Gnomad4 EAS

AF:

0.0190

Gnomad4 SAS

AF:

0.0192

Gnomad4 FIN

AF:

0.00354

Gnomad4 NFE

AF:

0.0172

Gnomad4 OTH

AF:

0.0385

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:9

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Townes-Brocks syndrome 1

Benign:4

Benign, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
Benign, criteria provided, single submitter	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	Sep 21, 2015	- -
Benign, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	Jan 10, 2022	- -
Benign, criteria provided, single submitter	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	May 20, 2016	- -

not specified

Benign:2

Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Likely benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Nov 12, 2014	- -

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 17, 2015	This variant is associated with the following publications: (PMID: 33226606) -
Likely benign, no assertion criteria provided	clinical testing	Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	-	- -

Townes syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 29, 2024

- -

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