dbSNP rs1965024: SALL1:p.Leu858Leu (chr16-51139648-G-A) – ACMG Classification: Benign (-21 pts)

Variant summary

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

The NM_002968.3(SALL1):c.2574C>T(p.Leu858Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.638 in 1,613,246 control chromosomes in the GnomAD database, including 338,355 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.52 ( 23760 hom., cov: 33)

Exomes 𝑓: 0.65 ( 314595 hom. )

Consequence

SALL1
NM_002968.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:10

Conservation

PhyloP100: -2.39

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 -21 ACMG points.

BP4

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

BP6

Variant 16-51139648-G-A is Benign according to our data. Variant chr16-51139648-G-A is described in ClinVar as [Benign]. Clinvar id is 258866.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-51139648-G-A is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-2.39 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SALL1	NM_002968.3 link	c.2574C>T	p.Leu858Leu	synonymous_variant	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.2574C>T	p.Leu858Leu	synonymous_variant	Exon 2 of 3	1	NM_002968.3	ENSP00000251020.4		Q9NSC2-1

Frequencies

GnomAD3 genomes

AF:

0.518

AC:

78718

AN:

151988

Hom.:

23755

Cov.:

show subpopulations

Gnomad AFR

AF:

0.184

Gnomad AMI

AF:

0.646

Gnomad AMR

AF:

0.606

Gnomad ASJ

AF:

0.526

Gnomad EAS

AF:

0.713

Gnomad SAS

AF:

0.735

Gnomad FIN

AF:

0.618

Gnomad MID

AF:

0.494

Gnomad NFE

AF:

0.653

Gnomad OTH

AF:

0.532

GnomAD3 exomes

AF:

0.626

AC:

157353

AN:

251370

Hom.:

51414

AF XY:

0.638

AC XY:

86713

AN XY:

135850

show subpopulations

Gnomad AFR exome

AF:

0.172

Gnomad AMR exome

AF:

0.653

Gnomad ASJ exome

AF:

0.522

Gnomad EAS exome

AF:

0.708

Gnomad SAS exome

AF:

0.733

Gnomad FIN exome

AF:

0.632

Gnomad NFE exome

AF:

0.649

Gnomad OTH exome

AF:

0.623

GnomAD4 exome

AF:

0.650

AC:

950250

AN:

1461140

Hom.:

314595

Cov.:

AF XY:

0.654

AC XY:

475254

AN XY:

726798

show subpopulations

Gnomad4 AFR exome

AF:

0.165

Gnomad4 AMR exome

AF:

0.649

Gnomad4 ASJ exome

AF:

0.521

Gnomad4 EAS exome

AF:

0.728

Gnomad4 SAS exome

AF:

0.733

Gnomad4 FIN exome

AF:

0.635

Gnomad4 NFE exome

AF:

0.662

Gnomad4 OTH exome

AF:

0.629

GnomAD4 genome

AF:

0.518

AC:

78721

AN:

152106

Hom.:

23760

Cov.:

AF XY:

0.523

AC XY:

38875

AN XY:

74364

show subpopulations

Gnomad4 AFR

AF:

0.183

Gnomad4 AMR

AF:

0.607

Gnomad4 ASJ

AF:

0.526

Gnomad4 EAS

AF:

0.714

Gnomad4 SAS

AF:

0.735

Gnomad4 FIN

AF:

0.618

Gnomad4 NFE

AF:

0.653

Gnomad4 OTH

AF:

0.532

Alfa

AF:

0.569

Hom.:

12268

Bravo

AF:

0.501

Asia WGS

AF:

0.698

AC:

2424

AN:

3478

EpiCase

AF:

0.640

EpiControl

AF:

0.638

ClinVar

Significance: Benign

Submissions summary: Benign:10

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Townes-Brocks syndrome 1

Benign:4

Nov 07, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Sep 21, 2015

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

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jun 21, 2017

Genome Diagnostics Laboratory, University Medical Center Utrecht

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified

Benign:3

Nov 24, 2015

Eurofins Ntd Llc (ga)

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

not provided

Benign:2

Mar 03, 2015

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Townes syndrome

Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.047

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