rs6882292

chr5-147877993-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000504320.5(SCGB3A2):c.-80-3453G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0727 in 152,206 control chromosomes in the GnomAD database, including 421 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 0.073 (421 hom., cov: 33)
• Consequence: SCGB3A2 ENST00000504320.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0827 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCGB3A2	ENST00000504320.5	c.-80-3453G>A		intron_variant		3
SCGB3A2	ENST00000507160.5	n.183-3453G>A		intron_variant, non_coding_transcript_variant		3
SCGB3A2	ENST00000514688.1	n.305-3453G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0727 AC: 11055 AN: 152088 Hom.: 422 Cov.: 33

Gnomad AFR AF: 0.0849

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0611

Gnomad ASJ AF: 0.0850

Gnomad EAS AF: 0.0559

Gnomad SAS AF: 0.0600

Gnomad FIN AF: 0.0653

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0706

Gnomad OTH AF: 0.0880

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0727 AC: 11068 AN: 152206 Hom.: 421 Cov.: 33 AF XY: 0.0716 AC XY: 5326 AN XY: 74420

Gnomad4 AFR AF: 0.0851

Gnomad4 AMR AF: 0.0611

Gnomad4 ASJ AF: 0.0850

Gnomad4 EAS AF: 0.0556

Gnomad4 SAS AF: 0.0599

Gnomad4 FIN AF: 0.0653

Gnomad4 NFE AF: 0.0706

Gnomad4 OTH AF: 0.0880

Alfa AF: 0.0795 Hom.: 81

Bravo AF: 0.0725

Asia WGS AF: 0.0440 AC: 154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.13
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6882292; hg19: chr5-147257556;