16-51136523-CA-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_002968.3(SALL1):c.*588del variant causes a 3 prime UTR change. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.54 (26106 hom., cov: 0)
  • Exomes 𝑓: 0.67 (128 hom.)
• Consequence: SALL1 NM_002968.3 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 5.34

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 16-51136523-CA-C is Benign according to our data. Variant chr16-51136523-CA-C is described in ClinVar as [Benign]. Clinvar id is 319586.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.738 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SALL1	NM_002968.3	c.*588del		3_prime_UTR_variant	3/3	ENST00000251020.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SALL1	ENST00000251020.9	c.*588del		3_prime_UTR_variant	3/3	1	NM_002968.3	P2
SALL1	ENST00000440970.6	c.*588del		3_prime_UTR_variant	4/4	5		P2
SALL1	ENST00000685868.1	c.*588del		3_prime_UTR_variant	4/4			P2

Frequencies

GnomAD3 genomes AF: 0.545 AC: 82251 AN: 150996 Hom.: 26102 Cov.: 0

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.759

Gnomad FIN AF: 0.731

Gnomad MID AF: 0.529

Gnomad NFE AF: 0.680

Gnomad OTH AF: 0.560

GnomAD4 exome AF: 0.669 AC: 376 AN: 562 Hom.: 128 Cov.: 0 AF XY: 0.640 AC XY: 210 AN XY: 328

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.594

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.685

Gnomad4 NFE exome AF: 0.659

Gnomad4 OTH exome AF: 0.667

GnomAD4 genome AF: 0.544 AC: 82252 AN: 151106 Hom.: 26106 Cov.: 0 AF XY: 0.554 AC XY: 40857 AN XY: 73814

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.628

Gnomad4 ASJ AF: 0.595

Gnomad4 EAS AF: 0.714

Gnomad4 SAS AF: 0.759

Gnomad4 FIN AF: 0.731

Gnomad4 NFE AF: 0.680

Gnomad4 OTH AF: 0.560

Bravo AF: 0.515

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Townes-Brocks syndrome 1 Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

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Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs35929381; hg19: chr16-51170434;