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GeneBe

19-5649932-C-T

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001201338.2(SAFB):c.1155C>T(p.Pro385=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00395 in 1,613,702 control chromosomes in the GnomAD database, including 198 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0067 ( 38 hom., cov: 31)
Exomes 𝑓: 0.0037 ( 160 hom. )

Consequence

SAFB
NM_001201338.2 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.82
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]

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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 (BayesDel_noAF=-0.55).
BP6
Variant 19-5649932-C-T is Benign according to our data. Variant chr19-5649932-C-T is described in ClinVar as [Benign]. Clinvar id is 735932.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.83 with no splicing effect.
BS2
High AC in GnomAd4 at 1026 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SAFBNM_001201338.2 linkuse as main transcriptc.1155C>T p.Pro385= synonymous_variant 8/21 ENST00000588852.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SAFBENST00000588852.2 linkuse as main transcriptc.1155C>T p.Pro385= synonymous_variant 8/211 NM_001201338.2 P5Q15424-3

Frequencies

GnomAD3 genomes
AF:
0.00674
AC:
1026
AN:
152116
Hom.:
38
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0000483
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000655
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.0106
Gnomad SAS
AF:
0.00208
Gnomad FIN
AF:
0.0773
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00193
Gnomad OTH
AF:
0.00382
GnomAD3 exomes
AF:
0.00847
AC:
2131
AN:
251452
Hom.:
60
AF XY:
0.00829
AC XY:
1126
AN XY:
135904
show subpopulations
Gnomad AFR exome
AF:
0.0000615
Gnomad AMR exome
AF:
0.0000867
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0103
Gnomad SAS exome
AF:
0.00137
Gnomad FIN exome
AF:
0.0738
Gnomad NFE exome
AF:
0.00207
Gnomad OTH exome
AF:
0.00994
GnomAD4 exome
AF:
0.00366
AC:
5349
AN:
1461468
Hom.:
160
Cov.:
30
AF XY:
0.00362
AC XY:
2634
AN XY:
727088
show subpopulations
Gnomad4 AFR exome
AF:
0.0000896
Gnomad4 AMR exome
AF:
0.0000671
Gnomad4 ASJ exome
AF:
0.0000383
Gnomad4 EAS exome
AF:
0.0109
Gnomad4 SAS exome
AF:
0.00151
Gnomad4 FIN exome
AF:
0.0725
Gnomad4 NFE exome
AF:
0.000596
Gnomad4 OTH exome
AF:
0.00404
GnomAD4 genome
AF:
0.00674
AC:
1026
AN:
152234
Hom.:
38
Cov.:
31
AF XY:
0.0101
AC XY:
752
AN XY:
74422
show subpopulations
Gnomad4 AFR
AF:
0.0000482
Gnomad4 AMR
AF:
0.0000654
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.0106
Gnomad4 SAS
AF:
0.00208
Gnomad4 FIN
AF:
0.0773
Gnomad4 NFE
AF:
0.00193
Gnomad4 OTH
AF:
0.00378
Alfa
AF:
0.00190
Hom.:
1
Bravo
AF:
0.000914
Asia WGS
AF:
0.0110
AC:
37
AN:
3478

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 testingInvitaeJul 17, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.55
CADD
Benign
5.3
DANN
Benign
0.62
RBP_binding_hub_radar
0.92
RBP_regulation_power_radar
2.8

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs75289952; hg19: chr19-5649943; COSMIC: COSV52651506; COSMIC: COSV52651506; API