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GeneBe

16-51137240-C-T

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 1P and 2B. PM2_SupportingBP4_Moderate

The NM_002968.3(SALL1):c.3847G>A(p.Glu1283Lys) variant causes a missense change. The variant was absent in control chromosomes in GnomAD Genomes project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 31)

Consequence

SALL1
NM_002968.3 missense

Scores

1
5
10

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 6.11

Links

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -1 ACMG points.

PM2
?
Very rare variant; Number of alleles below threshold, Median coverage is 31.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.21671402).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SALL1NM_002968.3 linkuse as main transcriptc.3847G>A p.Glu1283Lys missense_variant 3/3 ENST00000251020.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SALL1ENST00000251020.9 linkuse as main transcriptc.3847G>A p.Glu1283Lys missense_variant 3/31 NM_002968.3 P2Q9NSC2-1

Frequencies

GnomAD3 genomes
Cov.:
31

ClinVar

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

Submissions by phenotype

Townes-Brocks syndrome 1 Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingJohns Hopkins Genomics, Johns Hopkins UniversityMar 31, 2020This SALL1 variant is absent from a large population dataset and has not been reported in the literature, to our knowledge. Of three bioinformatics tools queried, two predicts that the substitution would be damaging while one predicts that it would be neutral. The glutamic acid residue at this position is evolutionarily conserved across higher order species, but not in fish and is not predicted to impact canonical exon 3 splicing. Due to lack of segregation and functional data, we consider the clinical significance of c.3847G>A to be uncertain at this time. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.37
BayesDel_addAF
Benign
-0.019
T
BayesDel_noAF
Benign
-0.27
Cadd
Uncertain
24
Dann
Uncertain
1.0
Eigen
Uncertain
0.34
Eigen_PC
Uncertain
0.47
FATHMM_MKL
Pathogenic
0.99
D
LIST_S2
Uncertain
0.93
D;D
M_CAP
Benign
0.020
T
MetaRNN
Benign
0.22
T;T
MetaSVM
Benign
-0.98
T
MutationTaster
Benign
1.0
D;D;D;D
PROVEAN
Benign
-1.8
N;N
REVEL
Benign
0.10
Sift
Benign
0.13
T;D
Sift4G
Benign
0.062
T;T
Polyphen
0.88
.;P
Vest4
0.26
MutPred
0.33
.;Gain of ubiquitination at E1283 (P = 0.0048);
MVP
0.21
MPC
0.27
ClinPred
0.82
D
GERP RS
5.8
Varity_R
0.28
gMVP
0.46

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: rs1962320101; hg19: chr16-51171151; API