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GeneBe

19-5661645-A-C

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2

The NM_001201338.2(SAFB):c.1990A>C(p.Met664Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000558 in 1,612,048 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000059 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000055 ( 0 hom. )

Consequence

SAFB
NM_001201338.2 missense

Scores

2
17

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.27
Variant links:
Genes affected
SAFB (HGNC:10520): (scaffold attachment factor B) This gene encodes a DNA-binding protein which has high specificity for scaffold or matrix attachment region DNA elements (S/MAR DNA). This protein is thought to be involved in attaching the base of chromatin loops to the nuclear matrix but there is conflicting evidence as to whether this protein is a component of chromatin or a nuclear matrix protein. Scaffold attachment factors are a specific subset of nuclear matrix proteins (NMP) that specifically bind to S/MAR. The encoded protein is thought to serve as a molecular base to assemble a 'transcriptosome complex' in the vicinity of actively transcribed genes. It is involved in the regulation of heat shock protein 27 transcription, can act as an estrogen receptor co-repressor and is a candidate for breast tumorigenesis. This gene is arranged head-to-head with a similar gene whose product has the same functions. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jan 2011]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.072968304).
BS2
High AC in GnomAd4 at 9 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SAFBNM_001201338.2 linkuse as main transcriptc.1990A>C p.Met664Leu missense_variant 15/21 ENST00000588852.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SAFBENST00000588852.2 linkuse as main transcriptc.1990A>C p.Met664Leu missense_variant 15/211 NM_001201338.2 P5Q15424-3

Frequencies

GnomAD3 genomes
AF:
0.0000592
AC:
9
AN:
152090
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00
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:
0.000471
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000588
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000135
AC:
33
AN:
244004
Hom.:
0
AF XY:
0.000127
AC XY:
17
AN XY:
133382
show subpopulations
Gnomad AFR exome
AF:
0.00
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:
0.000303
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000555
AC:
81
AN:
1459958
Hom.:
0
Cov.:
32
AF XY:
0.0000496
AC XY:
36
AN XY:
726350
show subpopulations
Gnomad4 AFR exome
AF:
0.00
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:
0.000153
Gnomad4 NFE exome
AF:
0.0000549
Gnomad4 OTH exome
AF:
0.000199
GnomAD4 genome
AF:
0.0000592
AC:
9
AN:
152090
Hom.:
0
Cov.:
32
AF XY:
0.0000673
AC XY:
5
AN XY:
74292
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.000471
Gnomad4 NFE
AF:
0.0000588
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.0000264
ExAC
AF:
0.000265
AC:
32
EpiCase
AF:
0.000109
EpiControl
AF:
0.0000593

ClinVar

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

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsDec 14, 2023The c.1990A>C (p.M664L) alteration is located in exon 15 (coding exon 15) of the SAFB gene. This alteration results from a A to C substitution at nucleotide position 1990, causing the methionine (M) at amino acid position 664 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.099
BayesDel_addAF
Benign
-0.45
T
BayesDel_noAF
Benign
-0.58
CADD
Benign
17
DANN
Benign
0.61
DEOGEN2
Benign
0.16
T;.;.;.;T
Eigen
Benign
-0.54
Eigen_PC
Benign
-0.40
FATHMM_MKL
Uncertain
0.87
D
LIST_S2
Benign
0.78
T;T;T;T;D
M_CAP
Benign
0.019
T
MetaRNN
Benign
0.073
T;T;T;T;T
MetaSVM
Benign
-0.99
T
MutationAssessor
Benign
1.4
L;.;.;L;.
MutationTaster
Benign
1.0
D;D;D;D;D;D
PrimateAI
Uncertain
0.65
T
PROVEAN
Benign
-1.6
N;.;N;.;.
REVEL
Benign
0.048
Sift
Benign
0.28
T;.;T;.;.
Sift4G
Benign
0.45
T;T;T;T;T
Polyphen
0.0
B;.;.;.;.
Vest4
0.28
MutPred
0.40
Loss of catalytic residue at M664 (P = 0.0042);.;.;Loss of catalytic residue at M664 (P = 0.0042);.;
MVP
0.34
MPC
0.73
ClinPred
0.059
T
GERP RS
3.1
RBP_binding_hub_radar
1.1
RBP_regulation_power_radar
2.8
Varity_R
0.097
gMVP
0.33

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: rs200332592; hg19: chr19-5661656; COSMIC: COSV99412833; COSMIC: COSV99412833; API