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16-51137215-T-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_002968.3(SALL1):c.3872A>G(p.Asn1291Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0102 in 152118 control chromosomes in the gnomAD Genomes database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.010 ( 14 hom., cov: 31)
Exomes 𝑓: 0.010 ( 22 hom. )

Consequence

SALL1
NM_002968.3 missense

Scores

15

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:8

Conservation

PhyloP100: 0.426

Links

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
?
Computational evidence support a benign effect (MetaRNN=0.0030624866).
BP6
?
Variant 16-51137215-T-C is Benign according to our data. Variant chr16-51137215-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 218510.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-51137215-T-C is described in Lovd as [Benign]. Variant chr16-51137215-T-C is described in Lovd as [Likely_benign].
BS1
?
Variant frequency is greater than expected. gnomad allele frequency = 0.0102 (1554/152118) while in subpopulation NFE AF= 0.0164 (1118/68016). AF 95% confidence interval is 0.0156. There are 14 homozygotes in gnomad. There are 714 alleles in male gnomad subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High AC in GnomAd at 1554 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SALL1NM_002968.3 linkuse as main transcriptc.3872A>G p.Asn1291Ser missense_variant 3/3 ENST00000251020.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SALL1ENST00000251020.9 linkuse as main transcriptc.3872A>G p.Asn1291Ser missense_variant 3/31 NM_002968.3 P2Q9NSC2-1

Frequencies

GnomAD3 genomes
AF:
0.0102
AC:
1554
AN:
152118
Hom.:
14
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.00338
Gnomad AMI
AF:
0.00548
Gnomad AMR
AF:
0.00903
Gnomad ASJ
AF:
0.00346
Gnomad EAS
AF:
0.000386
Gnomad SAS
AF:
0.00707
Gnomad FIN
AF:
0.00772
Gnomad MID
AF:
0.00949
Gnomad NFE
AF:
0.0164
Gnomad OTH
AF:
0.00960
GnomAD3 exomes
AF:
0.0103
AC:
2583
AN:
251466
Hom.:
22
AF XY:
0.0108
AC XY:
1474
AN XY:
135912
show subpopulations
Gnomad AFR exome
AF:
0.00295
Gnomad AMR exome
AF:
0.00882
Gnomad ASJ exome
AF:
0.00397
Gnomad EAS exome
AF:
0.000109
Gnomad SAS exome
AF:
0.00774
Gnomad FIN exome
AF:
0.00892
Gnomad NFE exome
AF:
0.0148
Gnomad OTH exome
AF:
0.0125
GnomAD4 exome
AF:
0.0130
AC:
19051
AN:
1461878
Hom.:
150
AF XY:
0.0130
AC XY:
9478
AN XY:
727236
show subpopulations
Gnomad4 AFR exome
AF:
0.00296
Gnomad4 AMR exome
AF:
0.00926
Gnomad4 ASJ exome
AF:
0.00432
Gnomad4 EAS exome
AF:
0.000101
Gnomad4 SAS exome
AF:
0.00765
Gnomad4 FIN exome
AF:
0.00848
Gnomad4 NFE exome
AF:
0.0149
Gnomad4 OTH exome
AF:
0.0106
Alfa
AF:
0.0129
Hom.:
4
Bravo
AF:
0.00968
TwinsUK
AF:
0.0146
AC:
54
ALSPAC
AF:
0.0150
AC:
58
ESP6500AA
AF:
0.00318
AC:
14
ESP6500EA
AF:
0.0155
AC:
133
ExAC
AF:
0.0100
AC:
1220
Asia WGS
AF:
0.00433
AC:
15
AN:
3478
EpiCase
AF:
0.0154
EpiControl
AF:
0.0159

ClinVar

Significance: Benign/Likely benign
Submissions summary: Benign:8
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:3
Likely benign, no assertion criteria providedclinical testingLaboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)-- -
Benign, criteria provided, single submitterclinical testingGeneDxMar 03, 2015- -
Benign, criteria provided, single submitterclinical testingAthena Diagnostics IncJul 02, 2019- -
not specified Benign:2
Benign, criteria provided, single submitterclinical testingGenomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of PhiladelphiaDec 31, 2014- -
Likely benign, criteria provided, single submitterclinical testingPreventionGenetics, Part of Exact Sciences-- -
Townes-Brocks syndrome 1 Benign:2
Benign, criteria provided, single submitterclinical testingGenome Diagnostics Laboratory, University Medical Center UtrechtOct 09, 2014- -
Benign, criteria provided, single submitterclinical testingClinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical CenterSep 21, 2015- -
Townes syndrome Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeOct 21, 2022- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.053
BayesDel_addAF
Benign
-0.70
T
BayesDel_noAF
Benign
-0.76
Cadd
Benign
0.0010
Dann
Benign
0.42
Eigen
Benign
-1.6
Eigen_PC
Benign
-1.5
FATHMM_MKL
Benign
0.13
N
LIST_S2
Benign
0.54
T;T
MetaRNN
Benign
0.0031
T;T
MetaSVM
Benign
-1.0
T
MutationTaster
Benign
0.98
D;N;N;N
PROVEAN
Benign
0.66
N;N
REVEL
Benign
0.19
Sift
Benign
1.0
T;T
Sift4G
Benign
0.70
T;T
Polyphen
0.0
.;B
Vest4
0.070
MPC
0.16
ClinPred
0.0018
T
GERP RS
-2.4
Varity_R
0.024
gMVP
0.19

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: rs74499562; hg19: chr16-51171126; API