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GeneBe

16-51136523-CA-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_002968.3(SALL1):c.*588del variant causes a 3 prime UTR change. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.54 ( 26102 hom., cov: 0)

Consequence

SALL1
NM_002968.3 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 5.34

Links

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6
?
Variant 16-51136523-CA-C is Benign according to our data. Variant chr16-51136523-CA-C is described in ClinVar as [Benign]. Clinvar id is 319586.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.738 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SALL1NM_002968.3 linkuse as main transcriptc.*588del 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.*588del 3_prime_UTR_variant 3/31 NM_002968.3 P2Q9NSC2-1
SALL1ENST00000440970.6 linkuse as main transcriptc.*588del 3_prime_UTR_variant 4/45 P2Q9NSC2-1
SALL1ENST00000685868.1 linkuse as main transcriptc.*588del 3_prime_UTR_variant 4/4 P2Q9NSC2-1

Frequencies

GnomAD3 genomes
AF:
0.545
AC:
82251
AN:
150996
Hom.:
26102
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.186
Gnomad AMI
AF:
0.645
Gnomad AMR
AF:
0.628
Gnomad ASJ
AF:
0.595
Gnomad EAS
AF:
0.713
Gnomad SAS
AF:
0.759
Gnomad FIN
AF:
0.731
Gnomad MID
AF:
0.529
Gnomad NFE
AF:
0.680
Gnomad OTH
AF:
0.560
GnomAD4 exome
AF:
0.669
AC:
376
AN:
562
Hom.:
128
AF XY:
0.640
AC XY:
210
AN XY:
328
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.594
Gnomad4 EAS exome
AF:
1.00
Gnomad4 SAS exome
AF:
0.500
Gnomad4 FIN exome
AF:
0.685
Gnomad4 NFE exome
AF:
0.659
Gnomad4 OTH exome
AF:
0.667
Bravo
AF:
0.515

ClinVar

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

Submissions by phenotype

Townes-Brocks syndrome 1 Benign:1
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: rs35929381; hg19: chr16-51170434; API