Genetic Variant SFSWAP:p.Asp388Asp (chr12-131753205-C-T) – ACMG Classification: Benign (-11 pts)

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

The NM_004592.4(SFSWAP):c.1164C>T(p.Asp388Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 1,613,950 control chromosomes in the GnomAD database, including 54,946 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 0.18 ( 3391 hom., cov: 33)

Exomes 𝑓: 0.25 ( 51555 hom. )

Consequence

SFSWAP
NM_004592.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.06

Publications

18 publications found

Variant links:

Genes affected

SFSWAP (HGNC:10790): (splicing factor SWAP) This gene encodes a human homolog of Drosophila splicing regulatory protein. This gene autoregulates its expression by control of splicing of its first two introns. In addition, it also regulates the splicing of fibronectin and CD45 genes. Two transcript variants encoding different isoforms have been identified. [provided by RefSeq, May 2012]

SFSWAP links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -11 ACMG points.

BP4

Computational evidence support a benign effect (REVEL=0.022).

BP7

Synonymous conserved (PhyloP=-1.06 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SFSWAP	NM_004592.4 link	c.1164C>T	p.Asp388Asp	synonymous_variant	Exon 8 of 18	ENST00000261674.9	NP_004583.2	Q12872-1Q8IV81

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SFSWAP	ENST00000261674.9 link	c.1164C>T	p.Asp388Asp	synonymous_variant	Exon 8 of 18	1	NM_004592.4	ENSP00000261674.4		Q12872-1

Frequencies

GnomAD3 genomes

AF:

0.184

AC:

27946

AN:

152094

Hom.:

3391

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0498

Gnomad AMI

AF:

0.240

Gnomad AMR

AF:

0.196

Gnomad ASJ

AF:

0.251

Gnomad EAS

AF:

0.00135

Gnomad SAS

AF:

0.126

Gnomad FIN

AF:

0.206

Gnomad MID

AF:

0.136

Gnomad NFE

AF:

0.272

Gnomad OTH

AF:

0.206

GnomAD2 exomes

AF:

0.197

AC:

49561

AN:

251482

AF XY:

0.201

show subpopulations

Gnomad AFR exome

AF:

0.0422

Gnomad AMR exome

AF:

0.151

Gnomad ASJ exome

AF:

0.267

Gnomad EAS exome

AF:

0.000815

Gnomad FIN exome

AF:

0.212

Gnomad NFE exome

AF:

0.270

Gnomad OTH exome

AF:

0.222

GnomAD4 exome

AF:

0.255

AC:

372718

AN:

1461738

Hom.:

51555

Cov.:

AF XY:

0.253

AC XY:

183656

AN XY:

727182

show subpopulations

African (AFR)

AF:

0.0385

AC:

1289

AN:

33480

American (AMR)

AF:

0.156

AC:

6970

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.262

AC:

6860

AN:

26136

East Asian (EAS)

AF:

0.000730

AC:

AN:

39700

South Asian (SAS)

AF:

0.140

AC:

12097

AN:

86254

European-Finnish (FIN)

AF:

0.215

AC:

11494

AN:

53418

Middle Eastern (MID)

AF:

0.170

AC:

979

AN:

5768

European-Non Finnish (NFE)

AF:

0.286

AC:

318542

AN:

1111868

Other (OTH)

AF:

0.239

AC:

14458

AN:

60390

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.462

Heterozygous variant carriers

15273

30546

45820

61093

76366

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10440

20880

31320

41760

52200

<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:

0.184

AC:

27954

AN:

152212

Hom.:

3391

Cov.:

AF XY:

0.179

AC XY:

13297

AN XY:

74404

show subpopulations

African (AFR)

AF:

0.0497

AC:

2063

AN:

41548

American (AMR)

AF:

0.196

AC:

3003

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.251

AC:

870

AN:

3472

East Asian (EAS)

AF:

0.00135

AC:

AN:

5178

South Asian (SAS)

AF:

0.127

AC:

614

AN:

4824

European-Finnish (FIN)

AF:

0.206

AC:

2188

AN:

10596

Middle Eastern (MID)

AF:

0.139

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.272

AC:

18517

AN:

67988

Other (OTH)

AF:

0.205

AC:

432

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1104

2207

3311

4414

5518

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

296

592

888

1184

1480

<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:

0.246

Hom.:

4753

Bravo

AF:

0.181

Asia WGS

AF:

0.0680

AC:

239

AN:

3478

EpiCase

AF:

0.269

EpiControl

AF:

0.275

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.62

CADD

Benign

0.91

(source)

DANN

Benign

0.94

PhyloP100

-1.1

PromoterAI

-0.13

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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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