Variant rs3741240 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003357.5(SCGB1A1):c.-26G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 1,564,120 control chromosomes in the GnomAD database, including 95,587 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

Frequency

Genomes: 𝑓 0.32 ( 7916 hom., cov: 31)

Exomes 𝑓: 0.35 ( 87671 hom. )

Consequence

SCGB1A1
NM_003357.5 5_prime_UTR

Scores

Clinical Significance

association no assertion criteria provided O:1

Conservation

PhyloP100: -0.268

Variant links:

Genes affected

SCGB1A1 (HGNC:12523): (secretoglobin family 1A member 1) This gene encodes a member of the secretoglobin family of small secreted proteins. The encoded protein has been implicated in numerous functions including anti-inflammation, inhibition of phospholipase A2 and the sequestering of hydrophobic ligands. Defects in this gene are associated with a susceptibility to asthma. [provided by RefSeq, May 2010]

SCGB1A1 links:

LOC102723765 (HGNC:):

LOC102723765 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=-0.88).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCGB1A1	NM_003357.5 linkuse as main transcript	c.-26G>A		5_prime_UTR_variant	1/3	ENST00000278282.3
LOC102723765	XR_007062699.1 linkuse as main transcript	n.238-2220C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCGB1A1	ENST00000278282.3 linkuse as main transcript	c.-26G>A		5_prime_UTR_variant	1/3	1	NM_003357.5	P1
SCGB1A1	ENST00000534397.5 linkuse as main transcript	c.-51+2433G>A		intron_variant		3

Frequencies

GnomAD3 genomes

AF:

0.321

AC:

48666

AN:

151822

Hom.:

7909

Cov.:

show subpopulations

Gnomad AFR

AF:

0.254

Gnomad AMI

AF:

0.283

Gnomad AMR

AF:

0.296

Gnomad ASJ

AF:

0.317

Gnomad EAS

AF:

0.370

Gnomad SAS

AF:

0.485

Gnomad FIN

AF:

0.360

Gnomad MID

AF:

0.247

Gnomad NFE

AF:

0.347

Gnomad OTH

AF:

0.300

GnomAD3 exomes

AF:

0.340

AC:

76958

AN:

226384

Hom.:

13642

AF XY:

0.349

AC XY:

42885

AN XY:

122710

show subpopulations

Gnomad AFR exome

AF:

0.242

Gnomad AMR exome

AF:

0.259

Gnomad ASJ exome

AF:

0.321

Gnomad EAS exome

AF:

0.358

Gnomad SAS exome

AF:

0.473

Gnomad FIN exome

AF:

0.350

Gnomad NFE exome

AF:

0.340

Gnomad OTH exome

AF:

0.323

GnomAD4 exome

AF:

0.349

AC:

492525

AN:

1412180

Hom.:

87671

Cov.:

AF XY:

0.353

AC XY:

247396

AN XY:

701130

show subpopulations

Gnomad4 AFR exome

AF:

0.246

Gnomad4 AMR exome

AF:

0.258

Gnomad4 ASJ exome

AF:

0.321

Gnomad4 EAS exome

AF:

0.383

Gnomad4 SAS exome

AF:

0.464

Gnomad4 FIN exome

AF:

0.348

Gnomad4 NFE exome

AF:

0.347

Gnomad4 OTH exome

AF:

0.341

GnomAD4 genome

AF:

0.320

AC:

48693

AN:

151940

Hom.:

7916

Cov.:

AF XY:

0.323

AC XY:

24016

AN XY:

74264

show subpopulations

Gnomad4 AFR

AF:

0.254

Gnomad4 AMR

AF:

0.295

Gnomad4 ASJ

AF:

0.317

Gnomad4 EAS

AF:

0.370

Gnomad4 SAS

AF:

0.484

Gnomad4 FIN

AF:

0.360

Gnomad4 NFE

AF:

0.347

Gnomad4 OTH

AF:

0.304

Alfa

AF:

0.338

Hom.:

12460

Bravo

AF:

0.304

Asia WGS

AF:

0.389

AC:

1352

AN:

3478

ClinVar

Significance: association

Submissions summary: Other:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Chronic obstructive pulmonary disease

Other:1

association, no assertion criteria provided

case-control

HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas

Feb 03, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.18

DANN

Benign

0.48

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

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