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GeneBe

16-51135999-C-CA

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PP3BP6_ModerateBS1BS2

The NM_002968.3(SALL1):c.*1112_*1113insT variant causes a 3 prime UTR change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00425 in 151458 control chromosomes in the gnomAD Genomes database, including 2 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0042 ( 2 hom., cov: 33)

Consequence

SALL1
NM_002968.3 3_prime_UTR

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 8.56

Links

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

PP3
?
No computational evidence supports a deleterious effect, but strongly conserved according to phyloP
BP6
?
Variant 16-51135999-C-CA is Benign according to our data. Variant chr16-51135999-C-CA is described in ClinVar as [Likely_benign]. Clinvar id is 319575.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected. gnomad allele frequency = 0.00425 (643/151458) while in subpopulation NFE AF= 0.0068 (461/67840). AF 95% confidence interval is 0.00628. There are 2 homozygotes in gnomad. There are 332 alleles in male gnomad subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd at 643 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SALL1NM_002968.3 linkuse as main transcriptc.*1112_*1113insT 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.*1112_*1113insT 3_prime_UTR_variant 3/31 NM_002968.3 P2Q9NSC2-1
SALL1ENST00000685868.1 linkuse as main transcriptc.*1112_*1113insT 3_prime_UTR_variant 4/4 P2Q9NSC2-1
SALL1ENST00000440970.6 linkuse as main transcript downstream_gene_variant 5 P2Q9NSC2-1

Frequencies

GnomAD3 genomes
AF:
0.00425
AC:
643
AN:
151458
Hom.:
2
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00157
Gnomad AMI
AF:
0.00330
Gnomad AMR
AF:
0.00263
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000772
Gnomad SAS
AF:
0.000626
Gnomad FIN
AF:
0.00570
Gnomad MID
AF:
0.00318
Gnomad NFE
AF:
0.00680
Gnomad OTH
AF:
0.00336
GnomAD4 exome
AF:
0.00231
AC:
1
AN:
432
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
260
show subpopulations
Gnomad4 FIN exome
AF:
0.00235
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
Bravo
AF:
0.00382

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

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

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs551203456; hg19: chr16-51169910; API