NM_002968.3:c.3456C>T

Variant names:

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_002968.3(SALL1):c.3456C>T(p.His1152His) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 1,613,986 control chromosomes in the GnomAD database, including 31,502 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.20 ( 3100 hom., cov: 33)

Exomes 𝑓: 0.19 ( 28402 hom. )

Consequence

SALL1
NM_002968.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:7

Conservation

PhyloP100: 0.0450

Publications

19 publications found

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 Gene-Disease associations (from GenCC):

Townes-Brocks syndrome 1
Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: PanelApp Australia, Labcorp Genetics (formerly Invitae), G2P, Ambry Genetics
Townes-Brocks syndrome
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

SALL1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.57).

BP6

Variant 16-51138766-G-A is Benign according to our data. Variant chr16-51138766-G-A is described in ClinVar as Benign. ClinVar VariationId is 258868.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.045 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002968.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SALL1	NM_002968.3	MANE Select	c.3456C>T	p.His1152His	synonymous	Exon 2 of 3	NP_002959.2
	SALL1	NM_001127892.2		c.3165C>T	p.His1055His	synonymous	Exon 2 of 3	NP_001121364.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
SALL1	ENST00000251020.9	TSL:1 MANE Select	c.3456C>T	p.His1152His	synonymous	Exon 2 of 3	ENSP00000251020.4
SALL1	ENST00000566102.1	TSL:1	c.77-1214C>T		intron	N/A	ENSP00000455582.1
SALL1	ENST00000440970.6	TSL:5	c.3456C>T	p.His1152His	synonymous	Exon 3 of 4	ENSP00000407914.2

Frequencies

GnomAD3 genomes

AF:

0.196

AC:

29778

AN:

152070

Hom.:

3096

Cov.:

show subpopulations

Gnomad AFR

AF:

0.180

Gnomad AMI

AF:

0.179

Gnomad AMR

AF:

0.178

Gnomad ASJ

AF:

0.260

Gnomad EAS

AF:

0.0337

Gnomad SAS

AF:

0.138

Gnomad FIN

AF:

0.269

Gnomad MID

AF:

0.294

Gnomad NFE

AF:

0.210

Gnomad OTH

AF:

0.215

GnomAD2 exomes

AF:

0.183

AC:

46040

AN:

251406

AF XY:

0.185

show subpopulations

Gnomad AFR exome

AF:

0.180

Gnomad AMR exome

AF:

0.132

Gnomad ASJ exome

AF:

0.268

Gnomad EAS exome

AF:

0.0328

Gnomad FIN exome

AF:

0.258

Gnomad NFE exome

AF:

0.211

Gnomad OTH exome

AF:

0.207

GnomAD4 exome

AF:

0.192

AC:

280177

AN:

1461798

Hom.:

28402

Cov.:

AF XY:

0.191

AC XY:

139235

AN XY:

727188

show subpopulations

African (AFR)

AF:

0.185

AC:

6198

AN:

33480

American (AMR)

AF:

0.138

AC:

6184

AN:

44720

Ashkenazi Jewish (ASJ)

AF:

0.270

AC:

7053

AN:

26136

East Asian (EAS)

AF:

0.0253

AC:

1005

AN:

39698

South Asian (SAS)

AF:

0.143

AC:

12370

AN:

86256

European-Finnish (FIN)

AF:

0.251

AC:

13434

AN:

53416

Middle Eastern (MID)

AF:

0.318

AC:

1830

AN:

5762

European-Non Finnish (NFE)

AF:

0.198

AC:

220500

AN:

1111934

Other (OTH)

AF:

0.192

AC:

11603

AN:

60396

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.484

Heterozygous variant carriers

13228

26456

39685

52913

66141

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7418

14836

22254

29672

37090

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.196

AC:

29796

AN:

152188

Hom.:

3100

Cov.:

AF XY:

0.196

AC XY:

14610

AN XY:

74406

show subpopulations

African (AFR)

AF:

0.180

AC:

7466

AN:

41514

American (AMR)

AF:

0.178

AC:

2726

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.260

AC:

904

AN:

3472

East Asian (EAS)

AF:

0.0334

AC:

173

AN:

5178

South Asian (SAS)

AF:

0.139

AC:

669

AN:

4820

European-Finnish (FIN)

AF:

0.269

AC:

2848

AN:

10576

Middle Eastern (MID)

AF:

0.303

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.210

AC:

14307

AN:

68006

Other (OTH)

AF:

0.213

AC:

451

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1234

2468

3701

4935

6169

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

320

640

960

1280

1600

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.201

Hom.:

12773

Bravo

AF:

0.187

Asia WGS

AF:

0.0830

AC:

288

AN:

3478

EpiCase

AF:

0.217

EpiControl

AF:

0.216

ClinVar

Significance: Benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

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

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

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 02, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Townes-Brocks syndrome 1

Benign:1

Nov 07, 2021

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.57

CADD

Benign

4.1

(source)

DANN

Benign

0.56

PhyloP100

0.045

Mutation Taster

=69/31

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over