Genetic Variant SALL1:p.Ser157_Ser159dup (chr16-51141744-C-CGCTGCTGCT) – ACMG Classification: Benign (-16 pts)

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2

The NM_002968.3(SALL1):c.469_477dupAGCAGCAGC(p.Ser157_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 0.00236 in 1,579,974 control chromosomes in the GnomAD database, including 17 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0039 ( 4 hom., cov: 31)

Exomes 𝑓: 0.0022 ( 13 hom. )

Consequence

SALL1
NM_002968.3 conservative_inframe_insertion

Scores

Not classified

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:6

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-CGCTGCTGCT is Benign according to our data. Variant chr16-51141744-C-CGCTGCTGCT is described in ClinVar as [Likely_benign]. Clinvar id is 702302.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00394 (595/151106) while in subpopulation SAS AF= 0.0239 (113/4734). AF 95% confidence interval is 0.0203. There are 4 homozygotes in gnomad4. There are 337 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.

BS2

High AC in GnomAd4 at 595 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SALL1	NM_002968.3 link	c.469_477dupAGCAGCAGC	p.Ser157_Ser159dup	conservative_inframe_insertion	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_477dupAGCAGCAGC	p.Ser157_Ser159dup	conservative_inframe_insertion	Exon 2 of 3	1	NM_002968.3	ENSP00000251020.4		Q9NSC2-1

Frequencies

GnomAD3 genomes

AF:

0.00391

AC:

591

AN:

150996

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00904

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00211

Gnomad ASJ

AF:

0.000580

Gnomad EAS

AF:

0.000390

Gnomad SAS

AF:

0.0238

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00962

Gnomad NFE

AF:

0.000916

Gnomad OTH

AF:

0.00288

GnomAD3 exomes

AF:

0.00446

AC:

952

AN:

213596

Hom.:

AF XY:

0.00516

AC XY:

595

AN XY:

115304

show subpopulations

Gnomad AFR exome

AF:

0.00889

Gnomad AMR exome

AF:

0.00201

Gnomad ASJ exome

AF:

0.000114

Gnomad EAS exome

AF:

0.000196

Gnomad SAS exome

AF:

0.0252

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000929

Gnomad OTH exome

AF:

0.00565

GnomAD4 exome

AF:

0.00219

AC:

3129

AN:

1428868

Hom.:

Cov.:

AF XY:

0.00273

AC XY:

1941

AN XY:

710672

show subpopulations

Gnomad4 AFR exome

AF:

0.00844

Gnomad4 AMR exome

AF:

0.00181

Gnomad4 ASJ exome

AF:

0.000118

Gnomad4 EAS exome

AF:

0.000104

Gnomad4 SAS exome

AF:

0.0210

Gnomad4 FIN exome

AF:

0.0000964

Gnomad4 NFE exome

AF:

0.000696

Gnomad4 OTH exome

AF:

0.00325

GnomAD4 genome

AF:

0.00394

AC:

595

AN:

151106

Hom.:

Cov.:

AF XY:

0.00457

AC XY:

337

AN XY:

73818

show subpopulations

Gnomad4 AFR

AF:

0.00907

Gnomad4 AMR

AF:

0.00210

Gnomad4 ASJ

AF:

0.000580

Gnomad4 EAS

AF:

0.000391

Gnomad4 SAS

AF:

0.0239

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000916

Gnomad4 OTH

AF:

0.00381

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Jul 26, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Mar 01, 2025

CeGaT Center for Human Genetics Tuebingen

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

SALL1: BS1, BS2 -

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:1

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Townes syndrome

Benign:1

Jan 14, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Townes-Brocks syndrome 1

Benign:1

Dec 09, 2021

Fulgent Genetics, Fulgent Genetics

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.

16-51141744-CGCTGCTGCTGCTGCTGCT-CGCTGCTGCTGCTGCTGCTGCTGCTGCT

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