dbSNP rs34212847: SCGB3A2:p.Val93Val (chr5-147882047-G-A) – ACMG Classification: Benign (-11 pts)

Variant summary

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

The NM_054023.5(SCGB3A2):c.279G>A(p.Val93Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00942 in 1,613,824 control chromosomes in the GnomAD database, including 439 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 0.018 ( 56 hom., cov: 32)

Exomes 𝑓: 0.0085 ( 383 hom. )

Consequence

SCGB3A2
NM_054023.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0700

Publications

8 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:

C5orf46 (HGNC:33768): (chromosome 5 open reading frame 46) Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

C5orf46 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 (BayesDel_noAF=-0.46).

BP7

Synonymous conserved (PhyloP=-0.07 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0682 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_054023.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCGB3A2	NM_054023.5	MANE Select	c.279G>A	p.Val93Val	synonymous	Exon 3 of 3	NP_473364.1	Q96PL1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
SCGB3A2	ENST00000296694.5	TSL:1 MANE Select	c.279G>A	p.Val93Val	synonymous	Exon 3 of 3	ENSP00000296694.4	Q96PL1
SCGB3A2	ENST00000937175.1		c.279G>A	p.Val93Val	synonymous	Exon 5 of 5	ENSP00000607234.1
SCGB3A2	ENST00000937176.1		c.279G>A	p.Val93Val	synonymous	Exon 4 of 4	ENSP00000607235.1

Frequencies

GnomAD3 genomes

AF:

0.0181

AC:

2761

AN:

152176

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0426

Gnomad AMI

AF:

0.0121

Gnomad AMR

AF:

0.00942

Gnomad ASJ

AF:

0.00807

Gnomad EAS

AF:

0.0740

Gnomad SAS

AF:

0.0358

Gnomad FIN

AF:

0.00113

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.00306

Gnomad OTH

AF:

0.0158

GnomAD2 exomes

AF:

0.0151

AC:

3802

AN:

251056

AF XY:

0.0152

show subpopulations

Gnomad AFR exome

AF:

0.0436

Gnomad AMR exome

AF:

0.00567

Gnomad ASJ exome

AF:

0.00546

Gnomad EAS exome

AF:

0.0769

Gnomad FIN exome

AF:

0.000786

Gnomad NFE exome

AF:

0.00263

Gnomad OTH exome

AF:

0.00767

GnomAD4 exome

AF:

0.00851

AC:

12431

AN:

1461530

Hom.:

383

Cov.:

AF XY:

0.00907

AC XY:

6598

AN XY:

727058

show subpopulations

African (AFR)

AF:

0.0494

AC:

1653

AN:

33456

American (AMR)

AF:

0.00588

AC:

263

AN:

44710

Ashkenazi Jewish (ASJ)

AF:

0.00651

AC:

170

AN:

26128

East Asian (EAS)

AF:

0.0973

AC:

3860

AN:

39682

South Asian (SAS)

AF:

0.0357

AC:

3078

AN:

86228

European-Finnish (FIN)

AF:

0.000843

AC:

AN:

53406

Middle Eastern (MID)

AF:

0.0116

AC:

AN:

5766

European-Non Finnish (NFE)

AF:

0.00235

AC:

2613

AN:

1111784

Other (OTH)

AF:

0.0113

AC:

682

AN:

60370

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.465

Heterozygous variant carriers

563

1125

1688

2250

2813

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

200

400

600

800

1000

<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:

0.0181

AC:

2764

AN:

152294

Hom.:

Cov.:

AF XY:

0.0185

AC XY:

1375

AN XY:

74474

show subpopulations

African (AFR)

AF:

0.0425

AC:

1765

AN:

41550

American (AMR)

AF:

0.00941

AC:

144

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.00807

AC:

AN:

3468

East Asian (EAS)

AF:

0.0743

AC:

385

AN:

5180

South Asian (SAS)

AF:

0.0357

AC:

172

AN:

4824

European-Finnish (FIN)

AF:

0.00113

AC:

AN:

10620

Middle Eastern (MID)

AF:

0.00680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00306

AC:

208

AN:

68028

Other (OTH)

AF:

0.0175

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

126

252

377

503

629

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

128

160

<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:

0.00839

Hom.:

Bravo

AF:

0.0201

Asia WGS

AF:

0.0640

AC:

222

AN:

3476

EpiCase

AF:

0.00311

EpiControl

AF:

0.00290

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.46

CADD

Benign

2.0

(source)

DANN

Benign

0.79

PhyloP100

-0.070

Mutation Taster

=98/2

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over