Genetic Variant SWAP70:c.1081-47T>G (chr11-9738166-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_015055.4(SWAP70):c.1081-47T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 1,388,812 control chromosomes in the GnomAD database, including 224,917 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 0.56 ( 23762 hom., cov: 33)

Exomes 𝑓: 0.57 ( 201155 hom. )

Consequence

SWAP70
NM_015055.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0700

Publications

28 publications found

Variant links:

Genes affected

SWAP70 (HGNC:17070): (switching B cell complex subunit SWAP70) Enables cadherin binding activity. Predicted to be involved in regulation of actin polymerization or depolymerization. Predicted to act upstream of or within isotype switching. Located in actin cytoskeleton; cytoplasm; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

SWAP70 links:

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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=-0.81).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SWAP70	NM_015055.4 link	c.1081-47T>G		intron_variant	Intron 7 of 11	ENST00000318950.11	NP_055870.2	Q9UH65B3KUB9
SWAP70	NM_001297714.2 link	c.907-47T>G		intron_variant	Intron 6 of 10		NP_001284643.1	Q9UH65B3KUB9E7EMB1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SWAP70	ENST00000318950.11 link	c.1081-47T>G		intron_variant	Intron 7 of 11	1	NM_015055.4	ENSP00000315630.6		Q9UH65

Frequencies

GnomAD3 genomes

AF:

0.556

AC:

84466

AN:

151960

Hom.:

23758

Cov.:

show subpopulations

Gnomad AFR

AF:

0.490

Gnomad AMI

AF:

0.600

Gnomad AMR

AF:

0.542

Gnomad ASJ

AF:

0.658

Gnomad EAS

AF:

0.401

Gnomad SAS

AF:

0.474

Gnomad FIN

AF:

0.699

Gnomad MID

AF:

0.744

Gnomad NFE

AF:

0.587

Gnomad OTH

AF:

0.589

GnomAD2 exomes

AF:

0.572

AC:

106093

AN:

185626

AF XY:

0.572

show subpopulations

Gnomad AFR exome

AF:

0.495

Gnomad AMR exome

AF:

0.595

Gnomad ASJ exome

AF:

0.659

Gnomad EAS exome

AF:

0.399

Gnomad FIN exome

AF:

0.682

Gnomad NFE exome

AF:

0.588

Gnomad OTH exome

AF:

0.596

GnomAD4 exome

AF:

0.567

AC:

700877

AN:

1236734

Hom.:

201155

Cov.:

AF XY:

0.566

AC XY:

351168

AN XY:

620154

show subpopulations

African (AFR)

AF:

0.485

AC:

13467

AN:

27746

American (AMR)

AF:

0.585

AC:

19258

AN:

32924

Ashkenazi Jewish (ASJ)

AF:

0.652

AC:

14227

AN:

21824

East Asian (EAS)

AF:

0.385

AC:

14305

AN:

37162

South Asian (SAS)

AF:

0.503

AC:

35835

AN:

71306

European-Finnish (FIN)

AF:

0.677

AC:

34488

AN:

50974

Middle Eastern (MID)

AF:

0.674

AC:

3493

AN:

5184

European-Non Finnish (NFE)

AF:

0.572

AC:

535955

AN:

937218

Other (OTH)

AF:

0.570

AC:

29849

AN:

52396

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

13998

27997

41995

55994

69992

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

14176

28352

42528

56704

70880

<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:

0.556

AC:

84483

AN:

152078

Hom.:

23762

Cov.:

AF XY:

0.556

AC XY:

41358

AN XY:

74334

show subpopulations

African (AFR)

AF:

0.490

AC:

20300

AN:

41468

American (AMR)

AF:

0.542

AC:

8272

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.658

AC:

2284

AN:

3470

East Asian (EAS)

AF:

0.400

AC:

2069

AN:

5176

South Asian (SAS)

AF:

0.473

AC:

2278

AN:

4820

European-Finnish (FIN)

AF:

0.699

AC:

7385

AN:

10568

Middle Eastern (MID)

AF:

0.748

AC:

220

AN:

294

European-Non Finnish (NFE)

AF:

0.587

AC:

39880

AN:

67982

Other (OTH)

AF:

0.590

AC:

1248

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1947

3894

5840

7787

9734

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

720

1440

2160

2880

3600

<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:

0.579

Hom.:

52882

Bravo

AF:

0.546

Asia WGS

AF:

0.442

AC:

1541

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

3.7

(source)

DANN

Benign

0.73

PhyloP100

0.070

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

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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