Variant 5-147878599-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

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 made for transcript

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	Protein
SCGB3A2	ENST00000504320.5 linkuse as main transcript	c.-80-2847G>A	intron_variant	3	ENSP00000423930
SCGB3A2	ENST00000507160.5 linkuse as main transcript	n.183-2847G>A	intron_variant, non_coding_transcript_variant	3
SCGB3A2	ENST00000514688.1 linkuse as main transcript	n.305-2847G>A	intron_variant, non_coding_transcript_variant	3

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

Gnomad4 AFR exome

AF:

0.306

Gnomad4 AMR exome

AF:

0.345

Gnomad4 ASJ exome

AF:

0.131

Gnomad4 EAS exome

AF:

0.217

Gnomad4 SAS exome

AF:

0.140

Gnomad4 FIN exome

AF:

0.149

Gnomad4 NFE exome

AF:

0.136

Gnomad4 OTH exome

AF:

0.162

GnomAD4 genome

AF:

0.206

AC:

31322

AN:

152014

Hom.:

3788

Cov.:

AF XY:

0.209

AC XY:

15522

AN XY:

74300

show subpopulations

Gnomad4 AFR

AF:

0.314

Gnomad4 AMR

AF:

0.294

Gnomad4 ASJ

AF:

0.141

Gnomad4 EAS

AF:

0.201

Gnomad4 SAS

AF:

0.149

Gnomad4 FIN

AF:

0.154

Gnomad4 NFE

AF:

0.138

Gnomad4 OTH

AF:

0.206

Alfa

AF:

0.151

Hom.:

3923

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

risk factor, no assertion criteria provided

literature only

OMIM

Mar 01, 2002

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

DANN

Benign

0.72

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over