Genetic Variant SCGB3A2:c.-80-2847G>A (chr5-147878599-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 ENST00000504320.5(SCGB3A2):c.-80-2847G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 576,858 control chromosomes in the GnomAD database, including 10,029 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as risk factor (no stars).

Frequency

Genomes: 𝑓 0.21 ( 3788 hom., cov: 32)

Exomes 𝑓: 0.16 ( 6241 hom. )

Consequence

SCGB3A2
ENST00000504320.5 intron

Scores

Clinical Significance

risk factor no assertion criteria provided O:1

Conservation

PhyloP100: 1.21

Publications

28 publications found

Variant links:

Genes affected

SCGB3A2 (HGNC:18391): (secretoglobin family 3A member 2) The protein encoded by this gene is a secreted lung surfactant protein and a downstream target of thyroid transcription factor. A single nucleotide polymorphism in the promoter of this gene results in susceptibility to asthma.[provided by RefSeq, Mar 2010]

SCGB3A2 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=-0.78).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCGB3A2	NM_054023.5 link	c.-205G>A		upstream_gene_variant		ENST00000296694.5	NP_473364.1	Q96PL1Q2L6B3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
SCGB3A2	ENST00000504320.5 link	c.-80-2847G>A	intron_variant	Intron 1 of 2	3		ENSP00000423930.1	D6RBX5
SCGB3A2	ENST00000507160.5 link	n.183-2847G>A	intron_variant	Intron 1 of 2	3
SCGB3A2	ENST00000514688.1 link	n.305-2847G>A	intron_variant	Intron 1 of 2	3
SCGB3A2	ENST00000296694.5 link	c.-205G>A	upstream_gene_variant		1	NM_054023.5	ENSP00000296694.4	Q96PL1

Frequencies

GnomAD3 genomes

AF:

0.206

AC:

31253

AN:

151896

Hom.:

3768

Cov.:

show subpopulations

Gnomad AFR

AF:

0.314

Gnomad AMI

AF:

0.0659

Gnomad AMR

AF:

0.294

Gnomad ASJ

AF:

0.141

Gnomad EAS

AF:

0.201

Gnomad SAS

AF:

0.149

Gnomad FIN

AF:

0.154

Gnomad MID

AF:

0.117

Gnomad NFE

AF:

0.138

Gnomad OTH

AF:

0.199

GnomAD4 exome

AF:

0.159

AC:

67603

AN:

424844

Hom.:

6241

AF XY:

0.157

AC XY:

34939

AN XY:

223014

show subpopulations

African (AFR)

AF:

0.306

AC:

3719

AN:

12166

American (AMR)

AF:

0.345

AC:

6643

AN:

19232

Ashkenazi Jewish (ASJ)

AF:

0.131

AC:

1722

AN:

13116

East Asian (EAS)

AF:

0.217

AC:

6614

AN:

30518

South Asian (SAS)

AF:

0.140

AC:

5652

AN:

40266

European-Finnish (FIN)

AF:

0.149

AC:

4480

AN:

29990

Middle Eastern (MID)

AF:

0.135

AC:

334

AN:

2476

European-Non Finnish (NFE)

AF:

0.136

AC:

34408

AN:

252254

Other (OTH)

AF:

0.162

AC:

4031

AN:

24826

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

2575

5150

7725

10300

12875

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

310

620

930

1240

1550

<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:

0.206

AC:

31322

AN:

152014

Hom.:

3788

Cov.:

AF XY:

0.209

AC XY:

15522

AN XY:

74300

show subpopulations

African (AFR)

AF:

0.314

AC:

13017

AN:

41420

American (AMR)

AF:

0.294

AC:

4495

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.141

AC:

489

AN:

3472

East Asian (EAS)

AF:

0.201

AC:

1038

AN:

5166

South Asian (SAS)

AF:

0.149

AC:

717

AN:

4824

European-Finnish (FIN)

AF:

0.154

AC:

1630

AN:

10572

Middle Eastern (MID)

AF:

0.109

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.138

AC:

9410

AN:

67978

Other (OTH)

AF:

0.206

AC:

434

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1218

2436

3653

4871

6089

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

316

632

948

1264

1580

<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:

0.159

Hom.:

9388

Bravo

AF:

0.222

Asia WGS

AF:

0.203

AC:

706

AN:

3478

ClinVar

Significance: risk factor

Submissions summary: Other:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Inherited susceptibility to asthma

Other:1

Mar 01, 2002

OMIM

Significance:risk factor

Review Status:no assertion criteria provided

Collection Method:literature only

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

(source)

DANN

Benign

0.72

PhyloP100

1.2

PromoterAI

-0.0086

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over