Variant chr19-5610034-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BS1BS2

The ENST00000252542.9(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
ENST00000252542.9 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.364

Variant links:

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]

SAFB2 links:

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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	Protein	UniProt
SAFB2	NM_014649.3 linkuse as main transcript	c.1257C>T	p.Arg419=	synonymous_variant	9/21	ENST00000252542.9	NP_055464.1
SAFB2	XM_011528449.4 linkuse as main transcript	c.1257C>T	p.Arg419=	synonymous_variant	9/21		XP_011526751.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SAFB2	ENST00000252542.9 linkuse as main transcript	c.1257C>T	p.Arg419=	synonymous_variant	9/21	1	NM_014649.3	ENSP00000252542	P1	Q14151-1

Frequencies

GnomAD3 genomes

AF:

0.0234

AC:

3557

AN:

152150

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00613

Gnomad AMI

AF:

0.0570

Gnomad AMR

AF:

0.0174

Gnomad ASJ

AF:

0.0378

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.0133

Gnomad FIN

AF:

0.0509

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.0322

Gnomad OTH

AF:

0.0263

GnomAD3 exomes

AF:

0.0250

AC:

6276

AN:

251116

Hom.:

129

AF XY:

0.0256

AC XY:

3481

AN XY:

135780

show subpopulations

Gnomad AFR exome

AF:

0.00580

Gnomad AMR exome

AF:

0.0140

Gnomad ASJ exome

AF:

0.0357

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0160

Gnomad FIN exome

AF:

0.0475

Gnomad NFE exome

AF:

0.0322

Gnomad OTH exome

AF:

0.0284

GnomAD4 exome

AF:

0.0276

AC:

40392

AN:

1461784

Hom.:

681

Cov.:

AF XY:

0.0275

AC XY:

19972

AN XY:

727202

show subpopulations

Gnomad4 AFR exome

AF:

0.00433

Gnomad4 AMR exome

AF:

0.0145

Gnomad4 ASJ exome

AF:

0.0329

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.0161

Gnomad4 FIN exome

AF:

0.0478

Gnomad4 NFE exome

AF:

0.0297

Gnomad4 OTH exome

AF:

0.0256

GnomAD4 genome

AF:

0.0234

AC:

3557

AN:

152268

Hom.:

Cov.:

AF XY:

0.0239

AC XY:

1782

AN XY:

74448

show subpopulations

Gnomad4 AFR

AF:

0.00614

Gnomad4 AMR

AF:

0.0174

Gnomad4 ASJ

AF:

0.0378

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.0133

Gnomad4 FIN

AF:

0.0509

Gnomad4 NFE

AF:

0.0322

Gnomad4 OTH

AF:

0.0260

Alfa

AF:

0.0293

Hom.:

Bravo

AF:

0.0199

Asia WGS

AF:

0.00577

AC:

AN:

3478

EpiCase

AF:

0.0332

EpiControl

AF:

0.0315

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.47

CADD

Benign

6.8

DANN

Benign

0.75

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over