16-51137019-A-AGGGGC

Variant summary

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

The NM_002968.3(SALL1):c.*92_*93insGCCCC variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0263 in 932,742 control chromosomes in the GnomAD database, including 462 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.063 (48 hom., cov: 31)
  • Exomes 𝑓: 0.024 (414 hom.)
• Consequence: SALL1 NM_002968.3 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.456

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 16-51137019-A-AGGGGC is Benign according to our data. Variant chr16-51137019-A-AGGGGC is described in ClinVar as [Benign]. Clinvar id is 1249227.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0834 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SALL1	NM_002968.3	c.*92_*93insGCCCC		3_prime_UTR_variant	3/3	ENST00000251020.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SALL1	ENST00000251020.9	c.*92_*93insGCCCC		3_prime_UTR_variant	3/3	1	NM_002968.3	P2
SALL1	ENST00000440970.6	c.*92_*93insGCCCC		3_prime_UTR_variant	4/4	5		P2
SALL1	ENST00000685868.1	c.*92_*93insGCCCC		3_prime_UTR_variant	4/4			P2
SALL1	ENST00000566102.1			downstream_gene_variant		1

Frequencies

GnomAD3 genomes AF: 0.0628 AC: 3141 AN: 50002 Hom.: 48 Cov.: 31

Gnomad AFR AF: 0.0181

Gnomad AMI AF: 0.142

Gnomad AMR AF: 0.0892

Gnomad ASJ AF: 0.0544

Gnomad EAS AF: 0.00119

Gnomad SAS AF: 0.0105

Gnomad FIN AF: 0.0494

Gnomad MID AF: 0.0568

Gnomad NFE AF: 0.0864

Gnomad OTH AF: 0.0685

GnomAD4 exome AF: 0.0242 AC: 21374 AN: 882702 Hom.: 414 Cov.: 12 AF XY: 0.0237 AC XY: 10745 AN XY: 453942

Gnomad4 AFR exome AF: 0.00603

Gnomad4 AMR exome AF: 0.0201

Gnomad4 ASJ exome AF: 0.0214

Gnomad4 EAS exome AF: 0.0000583

Gnomad4 SAS exome AF: 0.00392

Gnomad4 FIN exome AF: 0.0142

Gnomad4 NFE exome AF: 0.0298

Gnomad4 OTH exome AF: 0.0218

GnomAD4 genome AF: 0.0627 AC: 3138 AN: 50040 Hom.: 48 Cov.: 31 AF XY: 0.0601 AC XY: 1399 AN XY: 23292

Gnomad4 AFR AF: 0.0181

Gnomad4 AMR AF: 0.0890

Gnomad4 ASJ AF: 0.0544

Gnomad4 EAS AF: 0.00119

Gnomad4 SAS AF: 0.0105

Gnomad4 FIN AF: 0.0494

Gnomad4 NFE AF: 0.0863

Gnomad4 OTH AF: 0.0676

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 03, 2015

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs374006676; hg19: chr16-51170930;