rs806706
Positions:
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BS1BS2
The NM_014649.3(SAFB2):c.1257C>T(p.Arg419=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0272 in 1,614,052 control chromosomes in the GnomAD database, including 743 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.023 ( 62 hom., cov: 31)
Exomes 𝑓: 0.028 ( 681 hom. )
Consequence
SAFB2
NM_014649.3 synonymous
NM_014649.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.364
Genes affected
SAFB2 (HGNC:21605): (scaffold attachment factor B2) The protein encoded by this gene, along with its paralog (scaffold attachment factor B1), is a repressor of estrogen receptor alpha. The encoded protein binds scaffold/matrix attachment region (S/MAR) DNA and is involved in cell cycle regulation, apoptosis, differentiation, the stress response, and regulation of immune genes. [provided by RefSeq, May 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
BP7
?
Synonymous conserved (PhyloP=0.364 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0234 (3557/152268) while in subpopulation NFE AF= 0.0322 (2188/68020). AF 95% confidence interval is 0.031. There are 62 homozygotes in gnomad4. There are 1782 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 3557 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SAFB2 | NM_014649.3 | c.1257C>T | p.Arg419= | synonymous_variant | 9/21 | ENST00000252542.9 | |
SAFB2 | XM_011528449.4 | c.1257C>T | p.Arg419= | synonymous_variant | 9/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SAFB2 | ENST00000252542.9 | c.1257C>T | p.Arg419= | synonymous_variant | 9/21 | 1 | NM_014649.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0234 AC: 3557AN: 152150Hom.: 62 Cov.: 31
GnomAD3 genomes
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GnomAD3 exomes AF: 0.0250 AC: 6276AN: 251116Hom.: 129 AF XY: 0.0256 AC XY: 3481AN XY: 135780
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GnomAD4 exome AF: 0.0276 AC: 40392AN: 1461784Hom.: 681 Cov.: 31 AF XY: 0.0275 AC XY: 19972AN XY: 727202
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GnomAD4 genome ? AF: 0.0234 AC: 3557AN: 152268Hom.: 62 Cov.: 31 AF XY: 0.0239 AC XY: 1782AN XY: 74448
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at