dbSNP rs2285963: SAFB2:c.2394+24C>T (chr19-5591724-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_014649.3(SAFB2):c.2394+24C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 1,608,754 control chromosomes in the GnomAD database, including 16,242 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 0.14 ( 1478 hom., cov: 31)

Exomes 𝑓: 0.14 ( 14764 hom. )

Consequence

SAFB2
NM_014649.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0340

Publications

8 publications found

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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.226 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SAFB2	NM_014649.3 link	c.2394+24C>T		intron_variant	Intron 17 of 20	ENST00000252542.9	NP_055464.1	Q14151-1
SAFB2	XM_011528449.4 link	c.2394+24C>T		intron_variant	Intron 17 of 20		XP_011526751.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SAFB2	ENST00000252542.9 link	c.2394+24C>T		intron_variant	Intron 17 of 20	1	NM_014649.3	ENSP00000252542.3		Q14151-1

Frequencies

GnomAD3 genomes

AF:

0.136

AC:

20650

AN:

151818

Hom.:

1479

Cov.:

show subpopulations

Gnomad AFR

AF:

0.148

Gnomad AMI

AF:

0.129

Gnomad AMR

AF:

0.130

Gnomad ASJ

AF:

0.124

Gnomad EAS

AF:

0.176

Gnomad SAS

AF:

0.236

Gnomad FIN

AF:

0.0999

Gnomad MID

AF:

0.123

Gnomad NFE

AF:

0.127

Gnomad OTH

AF:

0.120

GnomAD2 exomes

AF:

0.144

AC:

36011

AN:

250888

AF XY:

0.151

show subpopulations

Gnomad AFR exome

AF:

0.151

Gnomad AMR exome

AF:

0.110

Gnomad ASJ exome

AF:

0.134

Gnomad EAS exome

AF:

0.175

Gnomad FIN exome

AF:

0.0987

Gnomad NFE exome

AF:

0.129

Gnomad OTH exome

AF:

0.136

GnomAD4 exome

AF:

0.137

AC:

200054

AN:

1456818

Hom.:

14764

Cov.:

AF XY:

0.141

AC XY:

102162

AN XY:

725016

show subpopulations

African (AFR)

AF:

0.145

AC:

4850

AN:

33378

American (AMR)

AF:

0.114

AC:

5098

AN:

44708

Ashkenazi Jewish (ASJ)

AF:

0.129

AC:

3370

AN:

26114

East Asian (EAS)

AF:

0.218

AC:

8655

AN:

39654

South Asian (SAS)

AF:

0.243

AC:

20916

AN:

86114

European-Finnish (FIN)

AF:

0.103

AC:

5471

AN:

53324

Middle Eastern (MID)

AF:

0.146

AC:

840

AN:

5758

European-Non Finnish (NFE)

AF:

0.129

AC:

142393

AN:

1107584

Other (OTH)

AF:

0.141

AC:

8461

AN:

60184

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.468

Heterozygous variant carriers

7458

14916

22374

29832

37290

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5382

10764

16146

21528

26910

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.136

AC:

20658

AN:

151936

Hom.:

1478

Cov.:

AF XY:

0.137

AC XY:

10153

AN XY:

74256

show subpopulations

African (AFR)

AF:

0.148

AC:

6133

AN:

41420

American (AMR)

AF:

0.130

AC:

1979

AN:

15248

Ashkenazi Jewish (ASJ)

AF:

0.124

AC:

431

AN:

3468

East Asian (EAS)

AF:

0.175

AC:

903

AN:

5160

South Asian (SAS)

AF:

0.237

AC:

1137

AN:

4796

European-Finnish (FIN)

AF:

0.0999

AC:

1056

AN:

10574

Middle Eastern (MID)

AF:

0.133

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.127

AC:

8611

AN:

67960

Other (OTH)

AF:

0.120

AC:

252

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

892

1785

2677

3570

4462

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

248

496

744

992

1240

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.130

Hom.:

2591

Bravo

AF:

0.134

Asia WGS

AF:

0.186

AC:

647

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

2.4

(source)

DANN

Benign

0.86

PhyloP100

-0.034

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over