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GeneBe

16-51137124-G-C

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4BP6_ModerateBS1BS2

The NM_002968.3(SALL1):c.3963C>G(p.Ile1321Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000191 in 152140 control chromosomes in the gnomAD Genomes database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. I1321I) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.00019 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000048 ( 0 hom. )

Consequence

SALL1
NM_002968.3 missense

Scores

4
12

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.283

Links

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
?
Computational evidence support a benign effect (MetaRNN=0.27669138).
BP6
?
Variant 16-51137124-G-C is Benign according to our data. Variant chr16-51137124-G-C is described in ClinVar as [Benign]. Clinvar id is 1280309.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected. gnomad allele frequency = 0.000191 (29/152140) while in subpopulation AFR AF= 0.000676 (28/41416). AF 95% confidence interval is 0.00048. There are 0 homozygotes in gnomad. There are 17 alleles in male gnomad subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High AC in GnomAd at 29 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SALL1NM_002968.3 linkuse as main transcriptc.3963C>G p.Ile1321Met missense_variant 3/3 ENST00000251020.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SALL1ENST00000251020.9 linkuse as main transcriptc.3963C>G p.Ile1321Met missense_variant 3/31 NM_002968.3 P2Q9NSC2-1

Frequencies

GnomAD3 genomes
AF:
0.000191
AC:
29
AN:
152140
Hom.:
0
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.000676
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
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:
0.000479
GnomAD3 exomes
AF:
0.0000477
AC:
12
AN:
251430
Hom.:
0
AF XY:
0.0000294
AC XY:
4
AN XY:
135908
show subpopulations
Gnomad AFR exome
AF:
0.000739
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000123
AC:
18
AN:
1461860
Hom.:
0
AF XY:
0.00000550
AC XY:
4
AN XY:
727232
show subpopulations
Gnomad4 AFR exome
AF:
0.000508
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.0000166
Bravo
AF:
0.000219
ESP6500AA
AF:
0.000682
AC:
3
ESP6500EA
AF:
0.00
AC:
0
ExAC
AF:
0.0000824
AC:
10

ClinVar

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

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxOct 14, 2020- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.10
BayesDel_addAF
Benign
-0.21
T
BayesDel_noAF
Benign
-0.11
Cadd
Benign
18
Dann
Uncertain
0.99
Eigen
Benign
0.095
Eigen_PC
Benign
-0.053
FATHMM_MKL
Benign
0.44
N
LIST_S2
Benign
0.82
T;T
M_CAP
Benign
0.061
D
MetaRNN
Benign
0.28
T;T
MetaSVM
Benign
-0.74
T
MutationTaster
Benign
1.0
D;D;D;D
PROVEAN
Benign
-1.6
N;N
REVEL
Uncertain
0.41
Sift
Uncertain
0.011
D;D
Sift4G
Uncertain
0.023
D;D
Polyphen
1.0
.;D
Vest4
0.63
MVP
0.55
MPC
0.76
ClinPred
0.17
T
GERP RS
-1.2
Varity_R
0.39
gMVP
0.28

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: rs200583558; hg19: chr16-51171035; API