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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 0.00813 in 50078 control chromosomes in the gnomAD Genomes database, including 1 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0081 ( 1 hom., cov: 31)

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

Links

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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. gnomad allele frequency = 0.00813 (407/50078) while in subpopulation AFR AF= 0.0313 (387/12370). AF 95% confidence interval is 0.0287. There are 1 homozygotes in gnomad. There are 199 alleles in male gnomad subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High AC in GnomAd at 407 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.:
31
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
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