Variant chr16-51151128-CGT-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_002968.3(SALL1):c.76+36_76+37del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0296 in 1,475,558 control chromosomes in the GnomAD database, including 763 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.023 ( 73 hom., cov: 32)

Exomes 𝑓: 0.030 ( 690 hom. )

Consequence

SALL1
NM_002968.3 intron

Scores

Not classified

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 2.91

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:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 16-51151128-CGT-C is Benign according to our data. Variant chr16-51151128-CGT-C is described in ClinVar as [Likely_benign]. Clinvar id is 258878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-51151128-CGT-C is described in Lovd as [Benign].

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.023 (3494/151976) while in subpopulation NFE AF= 0.0354 (2401/67894). AF 95% confidence interval is 0.0342. There are 73 homozygotes in gnomad4. There are 1702 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High AC in GnomAd4 at 3494 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
SALL1	NM_002968.3 linkuse as main transcript	c.76+36_76+37del	intron_variant	ENST00000251020.9	NP_002959.2
SALL1	XM_047434442.1 linkuse as main transcript	c.76+36_76+37del	intron_variant		XP_047290398.1
SALL1	XM_047434443.1 linkuse as main transcript	c.76+36_76+37del	intron_variant		XP_047290399.1
SALL1	XM_047434444.1 linkuse as main transcript	c.76+36_76+37del	intron_variant		XP_047290400.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SALL1	ENST00000251020.9 linkuse as main transcript	c.76+36_76+37del		intron_variant		1	NM_002968.3	ENSP00000251020	P2	Q9NSC2-1

Frequencies

GnomAD3 genomes

AF:

0.0230

AC:

3496

AN:

151862

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00500

Gnomad AMI

AF:

0.0515

Gnomad AMR

AF:

0.0166

Gnomad ASJ

AF:

0.00779

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00707

Gnomad FIN

AF:

0.0463

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0354

Gnomad OTH

AF:

0.0173

GnomAD3 exomes

AF:

0.0282

AC:

4556

AN:

161520

Hom.:

AF XY:

0.0276

AC XY:

2400

AN XY:

86950

show subpopulations

Gnomad AFR exome

AF:

0.00868

Gnomad AMR exome

AF:

0.0124

Gnomad ASJ exome

AF:

0.00809

Gnomad EAS exome

AF:

0.00314

Gnomad SAS exome

AF:

0.0102

Gnomad FIN exome

AF:

0.0555

Gnomad NFE exome

AF:

0.0432

Gnomad OTH exome

AF:

0.0294

GnomAD4 exome

AF:

0.0303

AC:

40126

AN:

1323582

Hom.:

690

AF XY:

0.0299

AC XY:

19678

AN XY:

659066

show subpopulations

Gnomad4 AFR exome

AF:

0.00507

Gnomad4 AMR exome

AF:

0.0124

Gnomad4 ASJ exome

AF:

0.00826

Gnomad4 EAS exome

AF:

0.000936

Gnomad4 SAS exome

AF:

0.00902

Gnomad4 FIN exome

AF:

0.0501

Gnomad4 NFE exome

AF:

0.0344

Gnomad4 OTH exome

AF:

0.0255

GnomAD4 genome

AF:

0.0230

AC:

3494

AN:

151976

Hom.:

Cov.:

AF XY:

0.0229

AC XY:

1702

AN XY:

74272

show subpopulations

Gnomad4 AFR

AF:

0.00499

Gnomad4 AMR

AF:

0.0166

Gnomad4 ASJ

AF:

0.00779

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00686

Gnomad4 FIN

AF:

0.0463

Gnomad4 NFE

AF:

0.0354

Gnomad4 OTH

AF:

0.0171

Bravo

AF:

0.0201

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 03, 2015

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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