16-51137582-C-CAG

Position:

• chr16-51137582-C-CAG

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The NM_002968.3(SALL1):​c.3535-31_3535-30insCT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000652 in 1,503,168 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000086 (0 hom., cov: 31)
  • Exomes 𝑓: 0.000063 (0 hom.)
• Consequence: SALL1 NM_002968.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.256

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 -8 ACMG points.

• BS1: Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.0000864 (13/150440) while in subpopulation AMR AF= 0.000132 (2/15104). AF 95% confidence interval is 0.0000327. There are 0 homozygotes in gnomad4. There are 8 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 13 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SALL1	NM_002968.3	c.3535-31_3535-30insCT		intron_variant		ENST00000251020.9	NP_002959.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SALL1	ENST00000251020.9	c.3535-31_3535-30insCT		intron_variant		1	NM_002968.3	ENSP00000251020	P2

Frequencies

GnomAD3 genomes AF: 0.0000798 AC: 12 AN: 150332 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.0000733

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000133

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.0000985

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000740

Gnomad OTH AF: 0.000487

GnomAD4 exome AF: 0.0000628 AC: 85 AN: 1352728 Hom.: 0 Cov.: 17 AF XY: 0.0000650 AC XY: 44 AN XY: 676818

Gnomad4 AFR exome AF: 0.0000639

Gnomad4 AMR exome AF: 0.0000917

Gnomad4 ASJ exome AF: 0.0000399

Gnomad4 EAS exome AF: 0.0000780

Gnomad4 SAS exome AF: 0.0000363

Gnomad4 FIN exome AF: 0.000143

Gnomad4 NFE exome AF: 0.0000588

Gnomad4 OTH exome AF: 0.0000885

GnomAD4 genome AF: 0.0000864 AC: 13 AN: 150440 Hom.: 0 Cov.: 31 AF XY: 0.000109 AC XY: 8 AN XY: 73454

Gnomad4 AFR AF: 0.0000975

Gnomad4 AMR AF: 0.000132

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.0000985

Gnomad4 NFE AF: 0.0000740

Gnomad4 OTH AF: 0.000482

ClinVar

Not reported in ClinVar

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: rs142249003; hg19: chr16-51171493;