16-51137019-AGGGGC-A

Variant summary

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

The NM_002968.3(SALL1):​c.*88_*92del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000741 in 933,008 control chromosomes in the GnomAD database, including 4 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0081 ( 1 hom., cov: 0)
Exomes 𝑓: 0.00032 ( 3 hom. )

Consequence

SALL1
NM_002968.3 3_prime_UTR

Scores

Not classified

Clinical Significance

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

Conservation

PhyloP100: 1.65
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6
Variant 16-51137019-AGGGGC-A is Benign according to our data. Variant chr16-51137019-AGGGGC-A is described in ClinVar as [Likely_benign]. Clinvar id is 319593.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-51137019-AGGGGC-A is described in Lovd as [Benign].
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00814 (408/50116) while in subpopulation AFR AF= 0.0313 (388/12396). AF 95% confidence interval is 0.0287. There are 1 homozygotes in gnomad4. There are 200 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
High AC in GnomAd4 at 408 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SALL1NM_002968.3 linkuse as main transcriptc.*88_*92del 3_prime_UTR_variant 3/3 ENST00000251020.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SALL1ENST00000251020.9 linkuse as main transcriptc.*88_*92del 3_prime_UTR_variant 3/31 NM_002968.3 P2Q9NSC2-1
SALL1ENST00000440970.6 linkuse as main transcriptc.*88_*92del 3_prime_UTR_variant 4/45 P2Q9NSC2-1
SALL1ENST00000685868.1 linkuse as main transcriptc.*88_*92del 3_prime_UTR_variant 4/4 P2Q9NSC2-1
SALL1ENST00000566102.1 linkuse as main transcript downstream_gene_variant 1

Frequencies

GnomAD3 genomes
AF:
0.00813
AC:
407
AN:
50078
Hom.:
1
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.0313
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00440
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00446
GnomAD4 exome
AF:
0.000321
AC:
283
AN:
882892
Hom.:
3
AF XY:
0.000302
AC XY:
137
AN XY:
454038
show subpopulations
Gnomad4 AFR exome
AF:
0.00994
Gnomad4 AMR exome
AF:
0.000390
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000103
Gnomad4 FIN exome
AF:
0.0000252
Gnomad4 NFE exome
AF:
0.00000813
Gnomad4 OTH exome
AF:
0.000730
GnomAD4 genome
AF:
0.00814
AC:
408
AN:
50116
Hom.:
1
Cov.:
0
AF XY:
0.00857
AC XY:
200
AN XY:
23330
show subpopulations
Gnomad4 AFR
AF:
0.0313
Gnomad4 AMR
AF:
0.00440
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00441
Alfa
AF:
0.0000559
Hom.:
0
Bravo
AF:
0.00315

ClinVar

Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingGeneDxMar 31, 2019- -
Townes-Brocks syndrome 1 Benign:1
Likely benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJun 14, 2016- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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.

Other links and lift over

dbSNP: rs374006676; hg19: chr16-51170930; API